Starting phenix.real_space_refine on Wed May 28 20:09:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ttw_41613/05_2025/8ttw_41613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ttw_41613/05_2025/8ttw_41613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ttw_41613/05_2025/8ttw_41613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ttw_41613/05_2025/8ttw_41613.map" model { file = "/net/cci-nas-00/data/ceres_data/8ttw_41613/05_2025/8ttw_41613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ttw_41613/05_2025/8ttw_41613.cif" } resolution = 2.96 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= -0.001 sd= 0.043 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 153 5.16 5 C 19545 2.51 5 N 5199 2.21 5 O 6378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31275 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3554 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "B" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "C" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1710 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "D" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3554 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1710 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "H" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "I" Number of atoms: 3554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3554 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "J" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1710 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 201} Chain: "M" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "N" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "O" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "P" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "Q" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "R" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 812 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "f" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "r" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 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: 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: "z" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "0" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "3" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "4" 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: "5" 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: "6" 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: "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: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {'83J': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {'83J': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 91 Unusual residues: {'83J': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" C1 MAN b 4 " occ=0.93 ... (9 atoms not shown) pdb=" O6 MAN b 4 " occ=0.93 residue: pdb=" C1 MAN b 8 " occ=0.80 ... (9 atoms not shown) pdb=" O6 MAN b 8 " occ=0.80 residue: pdb=" C1 MAN b 9 " occ=0.85 ... (9 atoms not shown) pdb=" O6 MAN b 9 " occ=0.85 residue: pdb=" C1 MAN n 4 " occ=0.77 ... (9 atoms not shown) pdb=" O6 MAN n 4 " occ=0.77 residue: pdb=" C1 MAN n 8 " occ=0.74 ... (9 atoms not shown) pdb=" O6 MAN n 8 " occ=0.74 residue: pdb=" C1 MAN n 9 " occ=0.82 ... (9 atoms not shown) pdb=" O6 MAN n 9 " occ=0.82 residue: pdb=" C1 MAN z 4 " occ=0.90 ... (9 atoms not shown) pdb=" O6 MAN z 4 " occ=0.90 residue: pdb=" C1 MAN z 8 " occ=0.87 ... (9 atoms not shown) pdb=" O6 MAN z 8 " occ=0.87 residue: pdb=" C1 MAN z 9 " occ=0.79 ... (9 atoms not shown) pdb=" O6 MAN z 9 " occ=0.79 Time building chain proxies: 20.10, per 1000 atoms: 0.64 Number of scatterers: 31275 At special positions: 0 Unit cell: (196.248, 190.032, 149.184, 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 153 16.00 O 6378 8.00 N 5199 7.00 C 19545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.02 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.04 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.04 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.04 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 140 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN 3 5 " - " MAN 3 6 " " MAN b 4 " - " MAN b 5 " " MAN b 5 " - " MAN b 6 " " MAN b 8 " - " MAN b 9 " " MAN f 4 " - " MAN f 5 " " MAN f 5 " - " MAN f 6 " " MAN n 4 " - " MAN n 5 " " MAN n 5 " - " MAN n 6 " " MAN n 8 " - " MAN n 9 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN z 4 " - " MAN z 5 " " MAN z 5 " - " MAN z 6 " " MAN z 8 " - " MAN z 9 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 7 " - " MAN 3 8 " " BMA b 3 " - " MAN b 4 " " MAN b 7 " - " MAN b 10 " " BMA c 3 " - " MAN c 4 " " BMA f 3 " - " MAN f 4 " " MAN f 7 " - " MAN f 8 " " BMA n 3 " - " MAN n 4 " " MAN n 7 " - " MAN n 10 " " BMA o 3 " - " MAN o 4 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 8 " " BMA z 3 " - " MAN z 4 " " MAN z 7 " - " MAN z 10 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA 3 3 " - " MAN 3 7 " " MAN 3 7 " - " MAN 3 9 " " BMA b 3 " - " MAN b 7 " " MAN b 7 " - " MAN b 8 " " BMA c 3 " - " MAN c 5 " " BMA f 3 " - " MAN f 7 " " MAN f 7 " - " MAN f 9 " " BMA n 3 " - " MAN n 7 " " MAN n 7 " - " MAN n 8 " " BMA o 3 " - " MAN o 5 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 9 " " BMA z 3 " - " MAN z 7 " " MAN z 7 " - " MAN z 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN I 262 " " NAG 1 1 " - " ASN I 295 " " NAG 2 1 " - " ASN I 301 " " NAG 3 1 " - " ASN I 332 " " NAG 4 1 " - " ASN I 363 " " NAG 5 1 " - " ASN I 386 " " NAG 6 1 " - " ASN I 392 " " NAG 7 1 " - " ASN I 448 " " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 355 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 88 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 301 " - " ASN C 82B" " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 355 " " NAG E 603 " - " ASN E 339 " " NAG E 604 " - " ASN E 88 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG G 301 " - " ASN G 82B" " NAG I 601 " - " ASN I 133 " " NAG I 602 " - " ASN I 355 " " NAG I 603 " - " ASN I 339 " " NAG I 604 " - " ASN I 88 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 618 " " NAG K 301 " - " ASN K 82B" " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN B 637 " " NAG U 1 " - " ASN E 276 " " NAG V 1 " - " ASN F 637 " " NAG W 1 " - " ASN I 276 " " NAG X 1 " - " ASN J 637 " " NAG Y 1 " - " ASN A 156 " " NAG Z 1 " - " ASN A 160 " " NAG a 1 " - " ASN A 197 " " NAG b 1 " - " ASN A 234 " " NAG c 1 " - " ASN A 262 " " NAG d 1 " - " ASN A 295 " " NAG e 1 " - " ASN A 301 " " NAG f 1 " - " ASN A 332 " " NAG g 1 " - " ASN A 363 " " NAG h 1 " - " ASN A 386 " " NAG i 1 " - " ASN A 392 " " NAG j 1 " - " ASN A 448 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 197 " " NAG n 1 " - " ASN E 234 " " NAG o 1 " - " ASN E 262 " " NAG p 1 " - " ASN E 295 " " NAG q 1 " - " ASN E 301 " " NAG r 1 " - " ASN E 332 " " NAG s 1 " - " ASN E 363 " " NAG t 1 " - " ASN E 386 " " NAG u 1 " - " ASN E 392 " " NAG v 1 " - " ASN E 448 " " NAG w 1 " - " ASN I 156 " " NAG x 1 " - " ASN I 160 " " NAG y 1 " - " ASN I 197 " " NAG z 1 " - " ASN I 234 " Time building additional restraints: 10.43 Conformation dependent library (CDL) restraints added in 3.8 seconds 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6924 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 80 sheets defined 11.6% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.793A pdb=" N CYS A 74 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 removed outlier: 3.501A pdb=" N MET A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.612A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.781A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.703A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.871A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.025A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 removed outlier: 3.681A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 596 removed outlier: 4.128A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.643A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 661 Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.746A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 189 removed outlier: 3.550A pdb=" N GLU D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.636A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.965A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.601A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.575A pdb=" N VAL E 345 " --> pdb=" O THR E 341 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.918A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.027A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.673A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR F 586 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 649 removed outlier: 3.660A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 652 through 661 Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'H' and resid 121 through 127 removed outlier: 3.764A pdb=" N SER H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 189 removed outlier: 3.546A pdb=" N GLU H 187 " --> pdb=" O LYS H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 74 removed outlier: 3.777A pdb=" N CYS I 74 " --> pdb=" O THR I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 117 removed outlier: 4.177A pdb=" N THR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.603A pdb=" N LEU I 125 " --> pdb=" O LEU I 122 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS I 126 " --> pdb=" O THR I 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 122 through 126' Processing helix chain 'I' and resid 335 through 353 removed outlier: 3.557A pdb=" N VAL I 345 " --> pdb=" O THR I 341 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS I 352 " --> pdb=" O GLN I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.735A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG I 480 " --> pdb=" O ARG I 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 475 through 480' Processing helix chain 'J' and resid 523 through 527 removed outlier: 4.654A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 542 removed outlier: 4.058A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 585 removed outlier: 3.610A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG J 579 " --> pdb=" O GLN J 575 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG J 585 " --> pdb=" O LEU J 581 " (cutoff:3.500A) Processing helix chain 'J' and resid 585 through 596 removed outlier: 4.159A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN J 590 " --> pdb=" O TYR J 586 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 Processing helix chain 'J' and resid 638 through 649 removed outlier: 3.633A pdb=" N GLY J 644 " --> pdb=" O GLN J 640 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU J 647 " --> pdb=" O TYR J 643 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU J 648 " --> pdb=" O GLY J 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 652 through 661 Processing helix chain 'K' and resid 185 through 189 Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.784A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 3.545A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 removed outlier: 5.217A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 177 removed outlier: 3.701A pdb=" N SER A 158 " --> pdb=" O GLN A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.862A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.041A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.292A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 removed outlier: 3.611A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.847A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.292A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.567A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 413 through 416 Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.942A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377 removed outlier: 4.434A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.420A pdb=" N GLU C 10 " --> pdb=" O SER C 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.713A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN C 50 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 35 " --> pdb=" O GLN C 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB6, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.636A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 136 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 181 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.636A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 136 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C 176 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 152 through 154 removed outlier: 4.615A pdb=" N TYR C 194 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.340A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR D 49 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 116 through 118 removed outlier: 3.837A pdb=" N PHE D 118 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL D 133 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 175 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 153 through 155 removed outlier: 4.597A pdb=" N TRP D 148 " --> pdb=" O GLN D 155 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS D 145 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL D 205 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 498 removed outlier: 5.202A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.473A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 86 " --> pdb=" O VAL E 242 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.822A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 170 through 177 removed outlier: 3.705A pdb=" N SER E 158 " --> pdb=" O GLN E 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 200 through 203 removed outlier: 5.828A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.027A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.045A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.875A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.765A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 298 current: chain 'E' and resid 358 through 361 Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 274 removed outlier: 10.765A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.875A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.274A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 12.045A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 416 Processing sheet with id=AD3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.925A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 374 through 378 removed outlier: 4.452A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.442A pdb=" N GLU G 10 " --> pdb=" O SER G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.714A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN G 50 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL G 35 " --> pdb=" O GLN G 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD9, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.796A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 136 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 181 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 121 through 124 removed outlier: 3.796A pdb=" N GLY G 139 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 136 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR G 176 " --> pdb=" O ASP G 144 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 152 through 154 removed outlier: 4.604A pdb=" N TYR G 194 " --> pdb=" O VAL G 211 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE4, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.366A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 116 through 118 removed outlier: 3.815A pdb=" N PHE H 118 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL H 133 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU H 175 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.608A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS H 145 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 494 through 498 removed outlier: 5.177A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N TYR I 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N CYS J 604 " --> pdb=" O TYR I 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AE9, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AF1, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AF2, first strand: chain 'I' and resid 170 through 177 removed outlier: 3.684A pdb=" N SER I 158 " --> pdb=" O GLN I 130 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 200 through 203 removed outlier: 5.880A pdb=" N ALA I 200 " --> pdb=" O ALA I 433 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR I 435 " --> pdb=" O ALA I 200 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.005A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 12.290A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 284 through 298 current: chain 'I' and resid 358 through 361 Processing sheet with id=AF5, first strand: chain 'I' and resid 271 through 274 removed outlier: 10.807A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.290A pdb=" N PHE I 288 " --> pdb=" O ILE I 453 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ILE I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 443 through 456 current: chain 'I' and resid 413 through 416 Processing sheet with id=AF6, first strand: chain 'I' and resid 304 through 312 removed outlier: 6.941A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 374 through 378 removed outlier: 4.485A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.417A pdb=" N GLU K 10 " --> pdb=" O SER K 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.717A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN K 50 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL K 35 " --> pdb=" O GLN K 50 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AG3, first strand: chain 'K' and resid 121 through 124 removed outlier: 3.658A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA K 136 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 181 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 121 through 124 removed outlier: 3.658A pdb=" N GLY K 139 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA K 136 " --> pdb=" O VAL K 184 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR K 176 " --> pdb=" O ASP K 144 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 152 through 154 removed outlier: 4.619A pdb=" N TYR K 194 " --> pdb=" O VAL K 211 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.337A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.506A pdb=" N PHE L 118 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU L 175 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.599A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS L 145 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 6 through 7 removed outlier: 3.606A pdb=" N THR M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL M 20 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS M 22 " --> pdb=" O LEU M 78 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER M 79 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER M 70 " --> pdb=" O SER M 79 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.531A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA M 93 " --> pdb=" O THR M 35 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.531A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL M 109 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N THR M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 20 through 22 Processing sheet with id=AH5, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.698A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 6 through 7 removed outlier: 3.647A pdb=" N THR O 21 " --> pdb=" O SER O 7 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.526A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA O 93 " --> pdb=" O THR O 35 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP O 34 " --> pdb=" O TYR O 50 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.526A pdb=" N VAL O 12 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL O 109 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N CYS O 92 " --> pdb=" O TRP O 103 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP O 103 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR O 94 " --> pdb=" O ASP O 101 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 18 through 19 removed outlier: 3.621A pdb=" N SER O 79 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER O 70 " --> pdb=" O SER O 79 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P' and resid 20 through 22 Processing sheet with id=AI2, first strand: chain 'P' and resid 45 through 48 removed outlier: 6.726A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Q' and resid 6 through 7 removed outlier: 3.656A pdb=" N THR Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.528A pdb=" N VAL Q 12 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA Q 93 " --> pdb=" O THR Q 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.528A pdb=" N VAL Q 12 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL Q 109 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 103 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP Q 103 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR Q 94 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 67 through 68 Processing sheet with id=AI7, first strand: chain 'R' and resid 20 through 22 Processing sheet with id=AI8, first strand: chain 'R' and resid 45 through 48 removed outlier: 6.729A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR R 102 " --> pdb=" O TYR R 86 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2367 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: 11.32 Time building geometry restraints manager: 11.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4866 1.31 - 1.45: 9602 1.45 - 1.59: 17266 1.59 - 1.72: 0 1.72 - 1.86: 204 Bond restraints: 31938 Sorted by residual: bond pdb=" C12 83J A 605 " pdb=" N02 83J A 605 " ideal model delta sigma weight residual 1.339 1.454 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C12 83J I 605 " pdb=" N02 83J I 605 " ideal model delta sigma weight residual 1.339 1.454 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C12 83J E 605 " pdb=" N02 83J E 605 " ideal model delta sigma weight residual 1.339 1.453 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C13 83J E 605 " pdb=" N05 83J E 605 " ideal model delta sigma weight residual 1.353 1.458 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C13 83J I 605 " pdb=" N05 83J I 605 " ideal model delta sigma weight residual 1.353 1.458 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 31933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 43039 3.75 - 7.50: 357 7.50 - 11.25: 17 11.25 - 15.00: 3 15.00 - 18.75: 12 Bond angle restraints: 43428 Sorted by residual: angle pdb=" C13 83J A 605 " pdb=" C15 83J A 605 " pdb=" C20 83J A 605 " ideal model delta sigma weight residual 118.87 100.12 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C13 83J E 605 " pdb=" C15 83J E 605 " pdb=" C20 83J E 605 " ideal model delta sigma weight residual 118.87 100.18 18.69 3.00e+00 1.11e-01 3.88e+01 angle pdb=" C13 83J I 605 " pdb=" C15 83J I 605 " pdb=" C20 83J I 605 " ideal model delta sigma weight residual 118.87 100.20 18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C25 83J A 605 " pdb=" C22 83J A 605 " pdb=" O11 83J A 605 " ideal model delta sigma weight residual 124.45 105.98 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C25 83J E 605 " pdb=" C22 83J E 605 " pdb=" O11 83J E 605 " ideal model delta sigma weight residual 124.45 106.10 18.35 3.00e+00 1.11e-01 3.74e+01 ... (remaining 43423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 19355 29.88 - 59.76: 1525 59.76 - 89.64: 171 89.64 - 119.52: 36 119.52 - 149.39: 6 Dihedral angle restraints: 21093 sinusoidal: 10317 harmonic: 10776 Sorted by residual: dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 1.69 -87.69 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 179.17 -86.17 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 88 " pdb=" CB CYS P 88 " ideal model delta sinusoidal sigma weight residual 93.00 6.97 86.03 1 1.00e+01 1.00e-02 8.94e+01 ... (remaining 21090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5074 0.104 - 0.207: 235 0.207 - 0.311: 17 0.311 - 0.415: 6 0.415 - 0.518: 2 Chirality restraints: 5334 Sorted by residual: chirality pdb=" CA CYS E 196 " pdb=" N CYS E 196 " pdb=" C CYS E 196 " pdb=" CB CYS E 196 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" C1 NAG 4 1 " pdb=" ND2 ASN I 363 " pdb=" C2 NAG 4 1 " pdb=" O5 NAG 4 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 5331 not shown) Planarity restraints: 5364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR L 140 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C TYR L 140 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR L 140 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO L 141 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS I 205 " -0.020 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C CYS I 205 " 0.066 2.00e-02 2.50e+03 pdb=" O CYS I 205 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO I 206 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 205 " 0.019 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C CYS A 205 " -0.062 2.00e-02 2.50e+03 pdb=" O CYS A 205 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 206 " 0.021 2.00e-02 2.50e+03 ... (remaining 5361 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 383 2.54 - 3.13: 24507 3.13 - 3.72: 45146 3.72 - 4.31: 68814 4.31 - 4.90: 116490 Nonbonded interactions: 255340 Sorted by model distance: nonbonded pdb=" O3 NAG I 604 " pdb=" O7 NAG I 604 " model vdw 1.953 3.040 nonbonded pdb=" O3 NAG E 604 " pdb=" O7 NAG E 604 " model vdw 1.960 3.040 nonbonded pdb=" O3 NAG X 2 " pdb=" O7 NAG X 2 " model vdw 1.963 3.040 nonbonded pdb=" O3 NAG V 2 " pdb=" O7 NAG V 2 " model vdw 1.966 3.040 nonbonded pdb=" O3 NAG T 2 " pdb=" O7 NAG T 2 " model vdw 1.976 3.040 ... (remaining 255335 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: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'c' selection = chain 'o' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = (chain '3' and (resid 1 or resid 4 through 9)) selection = (chain 'b' and (resid 2 or resid 5 through 10)) selection = (chain 'f' and (resid 1 or resid 4 through 9)) selection = (chain 'n' and (resid 2 or resid 5 through 10)) selection = (chain 'r' and (resid 1 or resid 4 through 9)) selection = (chain 'z' and (resid 2 or resid 5 through 10)) } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.74 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 72.660 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.005 0.115 32148 Z= 0.259 Angle : 0.890 18.748 44007 Z= 0.399 Chirality : 0.050 0.518 5334 Planarity : 0.004 0.084 5301 Dihedral : 19.688 149.394 14016 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.52 % Favored : 91.80 % Rotamer: Outliers : 10.42 % Allowed : 30.06 % Favored : 59.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.02 % 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: -2.50 (0.13), residues: 3684 helix: -3.64 (0.18), residues: 426 sheet: -0.95 (0.16), residues: 1152 loop : -1.63 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 69 HIS 0.003 0.001 HIS I 66 PHE 0.009 0.001 PHE E 391 TYR 0.017 0.001 TYR H 91 ARG 0.006 0.000 ARG F 588 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 63) link_NAG-ASN : angle 2.55383 ( 189) link_ALPHA1-6 : bond 0.00379 ( 15) link_ALPHA1-6 : angle 2.12960 ( 45) link_BETA1-4 : bond 0.00390 ( 51) link_BETA1-4 : angle 1.94887 ( 153) link_ALPHA1-2 : bond 0.00248 ( 15) link_ALPHA1-2 : angle 2.03471 ( 45) link_ALPHA1-3 : bond 0.00306 ( 15) link_ALPHA1-3 : angle 2.17157 ( 45) hydrogen bonds : bond 0.27746 ( 844) hydrogen bonds : angle 11.24124 ( 2367) SS BOND : bond 0.00555 ( 51) SS BOND : angle 2.64816 ( 102) covalent geometry : bond 0.00532 (31938) covalent geometry : angle 0.85523 (43428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 338 poor density : 322 time to evaluate : 3.122 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: C 100 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8086 (mpt) REVERT: E 189 LYS cc_start: 0.7253 (tptt) cc_final: 0.6962 (tmtt) REVERT: E 360 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7813 (ptt-90) REVERT: F 616 ASN cc_start: 0.8235 (p0) cc_final: 0.7988 (p0) REVERT: G 105 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: H 61 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7159 (ptp-170) REVERT: K 100 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7726 (mtp) REVERT: L 79 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6475 (mp10) REVERT: L 107 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6198 (mmtt) outliers start: 338 outliers final: 307 residues processed: 644 average time/residue: 1.0682 time to fit residues: 850.5448 Evaluate side-chains 635 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 314 poor density : 321 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 124 GLN Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 576 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 127 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 107 LYS Chi-restraints excluded: chain H residue 137 ASN Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 149 ASP Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 172 VAL Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 SER Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 368 ASP Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 393 SER Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 457 ASP Chi-restraints excluded: chain I residue 501 CYS Chi-restraints excluded: chain J residue 520 LEU Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 661 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 23 SER Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 40 SER Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain P residue 97 SER Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 40 SER Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 74 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 188 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 289 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 175 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 335 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 630 GLN C 105 GLN D 3 GLN D 124 GLN D 166 GLN E 195 ASN F 630 GLN H 3 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** H 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 577 GLN J 630 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 GLN N 37 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 77 GLN P 51 ASN Q 77 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.221595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.164005 restraints weight = 32983.140| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 4.16 r_work: 0.3280 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 32148 Z= 0.270 Angle : 0.851 15.130 44007 Z= 0.411 Chirality : 0.052 0.299 5334 Planarity : 0.006 0.151 5301 Dihedral : 15.408 154.659 7850 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.36 % Favored : 92.13 % Rotamer: Outliers : 13.57 % Allowed : 26.18 % Favored : 60.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.13), residues: 3684 helix: -2.72 (0.21), residues: 435 sheet: -0.89 (0.14), residues: 1272 loop : -1.63 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 610 HIS 0.006 0.001 HIS I 105 PHE 0.014 0.002 PHE G 91 TYR 0.042 0.002 TYR H 140 ARG 0.005 0.001 ARG P 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 63) link_NAG-ASN : angle 2.79366 ( 189) link_ALPHA1-6 : bond 0.00428 ( 15) link_ALPHA1-6 : angle 2.07261 ( 45) link_BETA1-4 : bond 0.00551 ( 51) link_BETA1-4 : angle 2.25775 ( 153) link_ALPHA1-2 : bond 0.00532 ( 15) link_ALPHA1-2 : angle 1.86552 ( 45) link_ALPHA1-3 : bond 0.00607 ( 15) link_ALPHA1-3 : angle 1.70307 ( 45) hydrogen bonds : bond 0.06277 ( 844) hydrogen bonds : angle 7.31622 ( 2367) SS BOND : bond 0.00708 ( 51) SS BOND : angle 2.10483 ( 102) covalent geometry : bond 0.00649 (31938) covalent geometry : angle 0.81281 (43428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 440 poor density : 328 time to evaluate : 3.397 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: A 125 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8348 (mt) REVERT: A 325 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8301 (p0) REVERT: A 358 ILE cc_start: 0.8169 (pt) cc_final: 0.7955 (pp) REVERT: A 419 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7819 (ptm160) REVERT: A 456 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7666 (ttp-170) REVERT: C 30 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8431 (m-10) REVERT: D 11 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7157 (tp) REVERT: E 153 GLU cc_start: 0.7005 (tt0) cc_final: 0.6599 (pt0) REVERT: E 456 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7635 (mtp180) REVERT: F 535 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7502 (mmt) REVERT: F 624 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8050 (p0) REVERT: G 30 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8428 (m-10) REVERT: G 80 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8471 (tp) REVERT: G 100 ASP cc_start: 0.7739 (t0) cc_final: 0.7492 (m-30) REVERT: H 61 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6484 (ptt-90) REVERT: H 79 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.5769 (mp10) REVERT: I 100 MET cc_start: 0.8919 (mtp) cc_final: 0.8665 (mtp) REVERT: I 189 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.6417 (tmtt) REVERT: I 360 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8222 (ptt-90) REVERT: J 575 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8159 (tp-100) REVERT: J 640 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8338 (mp10) REVERT: J 654 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5832 (tt0) REVERT: K 13 LYS cc_start: 0.8186 (mmpt) cc_final: 0.7814 (mmtt) REVERT: L 61 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6592 (ptt-90) REVERT: L 79 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.5819 (mp10) REVERT: M 77 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: N 11 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6771 (mm) REVERT: N 50 ASN cc_start: 0.8171 (t0) cc_final: 0.7440 (t0) REVERT: O 29 MET cc_start: 0.3645 (OUTLIER) cc_final: 0.3396 (pmt) REVERT: O 77 GLN cc_start: 0.6577 (OUTLIER) cc_final: 0.6227 (pm20) REVERT: P 28 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6661 (mp) REVERT: P 50 ASN cc_start: 0.8111 (t0) cc_final: 0.7608 (t0) REVERT: Q 77 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6183 (pm20) outliers start: 440 outliers final: 263 residues processed: 701 average time/residue: 1.0726 time to fit residues: 926.6129 Evaluate side-chains 597 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 289 poor density : 308 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 365 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 456 ARG Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 278 THR Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 325 ASP Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 595 ILE Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 77 GLN Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 29 MET Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 77 GLN Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 21 ILE Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 77 GLN Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 359 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 344 optimal weight: 9.9990 chunk 341 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN F 577 GLN F 616 ASN G 6 GLN G 105 GLN H 3 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 ASN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN L 166 GLN N 37 GLN O 99 GLN P 37 GLN P 51 ASN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.223906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.170535 restraints weight = 33257.936| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.60 r_work: 0.3334 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 32148 Z= 0.197 Angle : 0.770 11.450 44007 Z= 0.372 Chirality : 0.050 0.292 5334 Planarity : 0.006 0.139 5301 Dihedral : 13.865 155.530 7660 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.38 % Favored : 93.21 % Rotamer: Outliers : 11.63 % Allowed : 28.52 % Favored : 59.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % 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: -2.16 (0.13), residues: 3684 helix: -2.27 (0.22), residues: 435 sheet: -0.87 (0.14), residues: 1275 loop : -1.58 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 610 HIS 0.004 0.001 HIS E 105 PHE 0.013 0.002 PHE L 118 TYR 0.033 0.002 TYR H 140 ARG 0.009 0.000 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 63) link_NAG-ASN : angle 2.68044 ( 189) link_ALPHA1-6 : bond 0.00354 ( 15) link_ALPHA1-6 : angle 1.89604 ( 45) link_BETA1-4 : bond 0.00374 ( 51) link_BETA1-4 : angle 2.10406 ( 153) link_ALPHA1-2 : bond 0.00492 ( 15) link_ALPHA1-2 : angle 1.81978 ( 45) link_ALPHA1-3 : bond 0.00696 ( 15) link_ALPHA1-3 : angle 1.51640 ( 45) hydrogen bonds : bond 0.04914 ( 844) hydrogen bonds : angle 6.54959 ( 2367) SS BOND : bond 0.00637 ( 51) SS BOND : angle 2.11815 ( 102) covalent geometry : bond 0.00470 (31938) covalent geometry : angle 0.73094 (43428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 377 poor density : 324 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8281 (mt) REVERT: A 456 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7509 (ttp-110) REVERT: B 658 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: C 30 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8452 (m-10) REVERT: D 11 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7326 (tp) REVERT: E 153 GLU cc_start: 0.6875 (tt0) cc_final: 0.6534 (tt0) REVERT: F 535 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7735 (mpp) REVERT: F 616 ASN cc_start: 0.8311 (p0) cc_final: 0.7994 (p0) REVERT: F 624 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7997 (p0) REVERT: F 658 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: G 30 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8433 (m-10) REVERT: G 100 ASP cc_start: 0.7678 (t0) cc_final: 0.7458 (m-30) REVERT: G 105 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7964 (pt0) REVERT: G 179 SER cc_start: 0.7515 (OUTLIER) cc_final: 0.6690 (p) REVERT: H 61 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6578 (ptt-90) REVERT: H 79 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.5805 (mp10) REVERT: I 84 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8454 (mp) REVERT: I 189 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.6421 (tmtt) REVERT: I 268 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7484 (mt-10) REVERT: I 360 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8148 (ptt-90) REVERT: J 575 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8060 (tp-100) REVERT: J 640 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: J 654 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5516 (tt0) REVERT: K 69 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7919 (mm) REVERT: L 61 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6605 (ptt-90) REVERT: L 79 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6133 (mp10) REVERT: N 11 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6757 (mm) REVERT: N 50 ASN cc_start: 0.8193 (t0) cc_final: 0.7722 (t0) REVERT: O 29 MET cc_start: 0.3636 (OUTLIER) cc_final: 0.3386 (pmt) REVERT: O 82 VAL cc_start: 0.3930 (OUTLIER) cc_final: 0.3278 (t) REVERT: P 28 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6724 (mp) REVERT: P 50 ASN cc_start: 0.8251 (t0) cc_final: 0.7654 (t0) outliers start: 377 outliers final: 225 residues processed: 637 average time/residue: 1.1100 time to fit residues: 870.2615 Evaluate side-chains 559 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 308 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 248 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain J residue 659 ASP Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 29 MET Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain Q residue 102 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 263 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 chunk 243 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 321 optimal weight: 0.8980 chunk 310 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 332 optimal weight: 20.0000 chunk 367 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN G 6 GLN G 105 GLN H 3 GLN I 183 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN L 166 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 77 GLN N 37 GLN O 3 GLN O 77 GLN O 99 GLN P 37 GLN P 51 ASN Q 3 GLN Q 77 GLN Q 99 GLN R 51 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.224488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.171297 restraints weight = 33312.394| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.61 r_work: 0.3340 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32148 Z= 0.182 Angle : 0.753 12.840 44007 Z= 0.359 Chirality : 0.049 0.301 5334 Planarity : 0.005 0.143 5301 Dihedral : 13.075 155.968 7594 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.79 % Favored : 92.81 % Rotamer: Outliers : 11.07 % Allowed : 28.95 % Favored : 59.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % 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: -2.07 (0.13), residues: 3684 helix: -1.98 (0.23), residues: 435 sheet: -0.89 (0.14), residues: 1299 loop : -1.52 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 610 HIS 0.004 0.001 HIS I 105 PHE 0.013 0.001 PHE G 91 TYR 0.027 0.002 TYR H 140 ARG 0.007 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 63) link_NAG-ASN : angle 2.63563 ( 189) link_ALPHA1-6 : bond 0.00375 ( 15) link_ALPHA1-6 : angle 1.88196 ( 45) link_BETA1-4 : bond 0.00381 ( 51) link_BETA1-4 : angle 2.08569 ( 153) link_ALPHA1-2 : bond 0.00481 ( 15) link_ALPHA1-2 : angle 1.81377 ( 45) link_ALPHA1-3 : bond 0.00714 ( 15) link_ALPHA1-3 : angle 1.55692 ( 45) hydrogen bonds : bond 0.04427 ( 844) hydrogen bonds : angle 6.15915 ( 2367) SS BOND : bond 0.00706 ( 51) SS BOND : angle 2.24497 ( 102) covalent geometry : bond 0.00435 (31938) covalent geometry : angle 0.71204 (43428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 359 poor density : 307 time to evaluate : 3.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8245 (mt) REVERT: A 419 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7728 (ptm160) REVERT: A 456 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7442 (ttp-110) REVERT: B 542 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7102 (ptt90) REVERT: B 658 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: C 30 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8331 (m-10) REVERT: C 69 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7985 (mm) REVERT: C 179 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.6727 (p) REVERT: D 11 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7307 (tp) REVERT: D 20 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7747 (mmm160) REVERT: D 166 GLN cc_start: 0.7684 (tt0) cc_final: 0.7229 (tt0) REVERT: E 153 GLU cc_start: 0.6835 (tt0) cc_final: 0.6575 (tt0) REVERT: F 535 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7708 (mpp) REVERT: F 658 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: G 30 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8428 (m-10) REVERT: G 100 ASP cc_start: 0.7648 (t0) cc_final: 0.7431 (m-30) REVERT: G 105 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7861 (pt0) REVERT: H 20 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7261 (mtm180) REVERT: H 47 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8507 (mt) REVERT: H 61 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6411 (ptt-90) REVERT: H 79 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.5725 (mp10) REVERT: I 75 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8406 (m) REVERT: I 84 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8449 (mp) REVERT: I 189 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.6413 (tmtt) REVERT: I 268 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7526 (mt-10) REVERT: I 360 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8170 (ptt-90) REVERT: J 575 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8034 (tp-100) REVERT: J 581 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8096 (tp) REVERT: J 616 ASN cc_start: 0.8178 (p0) cc_final: 0.7896 (p0) REVERT: J 640 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: J 654 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.5515 (tt0) REVERT: K 66 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8105 (ttt90) REVERT: K 69 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7883 (mm) REVERT: L 61 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6675 (ptt-90) REVERT: L 78 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7160 (tt) REVERT: L 79 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6120 (mp10) REVERT: L 107 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6235 (tptt) REVERT: M 100 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8276 (mt-10) REVERT: M 100 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.5957 (mmm) REVERT: N 11 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6822 (mm) REVERT: N 50 ASN cc_start: 0.8161 (t0) cc_final: 0.7638 (t0) REVERT: P 28 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6682 (mp) REVERT: P 50 ASN cc_start: 0.8280 (t0) cc_final: 0.7630 (t0) outliers start: 359 outliers final: 225 residues processed: 609 average time/residue: 1.0729 time to fit residues: 801.7220 Evaluate side-chains 559 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 299 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 581 LEU Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 25 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 185 optimal weight: 0.8980 chunk 301 optimal weight: 30.0000 chunk 175 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 365 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN G 6 GLN G 105 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN M 3 GLN M 99 GLN N 37 GLN O 3 GLN O 99 GLN P 37 GLN P 51 ASN Q 3 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.222779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168507 restraints weight = 32938.129| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 3.53 r_work: 0.3334 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 32148 Z= 0.230 Angle : 0.782 12.179 44007 Z= 0.372 Chirality : 0.050 0.299 5334 Planarity : 0.006 0.140 5301 Dihedral : 12.752 155.581 7562 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.00 % Favored : 92.62 % Rotamer: Outliers : 11.13 % Allowed : 28.83 % Favored : 60.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % 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: -2.09 (0.13), residues: 3684 helix: -1.95 (0.23), residues: 435 sheet: -0.85 (0.14), residues: 1293 loop : -1.60 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 610 HIS 0.005 0.001 HIS I 105 PHE 0.014 0.002 PHE G 91 TYR 0.023 0.002 TYR H 140 ARG 0.004 0.000 ARG A 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 63) link_NAG-ASN : angle 2.71041 ( 189) link_ALPHA1-6 : bond 0.00400 ( 15) link_ALPHA1-6 : angle 1.98304 ( 45) link_BETA1-4 : bond 0.00410 ( 51) link_BETA1-4 : angle 2.18070 ( 153) link_ALPHA1-2 : bond 0.00422 ( 15) link_ALPHA1-2 : angle 1.88043 ( 45) link_ALPHA1-3 : bond 0.00638 ( 15) link_ALPHA1-3 : angle 1.53625 ( 45) hydrogen bonds : bond 0.04624 ( 844) hydrogen bonds : angle 6.03566 ( 2367) SS BOND : bond 0.00805 ( 51) SS BOND : angle 2.33335 ( 102) covalent geometry : bond 0.00557 (31938) covalent geometry : angle 0.74049 (43428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 361 poor density : 304 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8271 (mt) REVERT: A 168 LYS cc_start: 0.7124 (mmmm) cc_final: 0.6590 (pptt) REVERT: A 419 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7752 (ptm160) REVERT: B 658 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: C 30 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8420 (m-10) REVERT: C 69 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7929 (mm) REVERT: C 105 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8078 (pm20) REVERT: C 179 SER cc_start: 0.7670 (OUTLIER) cc_final: 0.6796 (p) REVERT: D 11 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7357 (tp) REVERT: D 79 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6503 (mp10) REVERT: D 106 VAL cc_start: 0.6401 (OUTLIER) cc_final: 0.6032 (t) REVERT: E 153 GLU cc_start: 0.6857 (tt0) cc_final: 0.6359 (pt0) REVERT: F 535 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7808 (mpt) REVERT: F 542 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7527 (ptt90) REVERT: F 658 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: G 30 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8439 (m-10) REVERT: G 80 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8485 (tp) REVERT: G 100 ASP cc_start: 0.7687 (t0) cc_final: 0.7466 (m-30) REVERT: H 20 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7319 (mtm180) REVERT: H 61 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6711 (ptt-90) REVERT: H 79 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.5798 (mp10) REVERT: I 75 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8400 (m) REVERT: I 84 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8489 (mp) REVERT: I 205 CYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6555 (m) REVERT: I 360 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8144 (ptt-90) REVERT: J 575 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8036 (tp-100) REVERT: J 616 ASN cc_start: 0.8179 (p0) cc_final: 0.7866 (p0) REVERT: J 640 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: J 654 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5510 (tt0) REVERT: K 66 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8129 (ttt90) REVERT: L 79 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6201 (mp10) REVERT: M 100 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: M 100 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.5906 (mmm) REVERT: N 11 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6837 (mm) REVERT: N 50 ASN cc_start: 0.8251 (t0) cc_final: 0.7260 (t0) REVERT: O 97 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8199 (ttp-170) REVERT: O 100 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: P 37 GLN cc_start: 0.7137 (tt0) cc_final: 0.6707 (tp-100) REVERT: P 50 ASN cc_start: 0.8364 (t0) cc_final: 0.7721 (t0) REVERT: P 79 GLU cc_start: 0.5547 (OUTLIER) cc_final: 0.5345 (pp20) REVERT: R 90 MET cc_start: 0.8759 (tpp) cc_final: 0.8453 (mmt) outliers start: 361 outliers final: 234 residues processed: 605 average time/residue: 1.1338 time to fit residues: 845.5498 Evaluate side-chains 562 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 296 time to evaluate : 3.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 356 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 542 ARG Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 134 VAL Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 GLU Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 71 ARG Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 208 optimal weight: 0.5980 chunk 331 optimal weight: 7.9990 chunk 4 optimal weight: 0.0010 chunk 81 optimal weight: 4.9990 chunk 363 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 349 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 GLN D 124 GLN D 166 GLN F 616 ASN G 6 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 100 GLN K 6 GLN K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN M 3 GLN M 99 GLN N 37 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.224986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.171329 restraints weight = 33124.072| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.50 r_work: 0.3364 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32148 Z= 0.161 Angle : 0.717 11.193 44007 Z= 0.342 Chirality : 0.048 0.302 5334 Planarity : 0.005 0.136 5301 Dihedral : 11.995 156.186 7539 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.24 % Favored : 93.43 % Rotamer: Outliers : 9.93 % Allowed : 30.13 % Favored : 59.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3684 helix: -1.70 (0.24), residues: 435 sheet: -0.67 (0.14), residues: 1224 loop : -1.54 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 610 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE I 383 TYR 0.021 0.001 TYR H 140 ARG 0.004 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 63) link_NAG-ASN : angle 2.54985 ( 189) link_ALPHA1-6 : bond 0.00480 ( 15) link_ALPHA1-6 : angle 1.87565 ( 45) link_BETA1-4 : bond 0.00395 ( 51) link_BETA1-4 : angle 2.02908 ( 153) link_ALPHA1-2 : bond 0.00502 ( 15) link_ALPHA1-2 : angle 1.78300 ( 45) link_ALPHA1-3 : bond 0.00746 ( 15) link_ALPHA1-3 : angle 1.50523 ( 45) hydrogen bonds : bond 0.04011 ( 844) hydrogen bonds : angle 5.77366 ( 2367) SS BOND : bond 0.00592 ( 51) SS BOND : angle 2.08736 ( 102) covalent geometry : bond 0.00385 (31938) covalent geometry : angle 0.67670 (43428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 322 poor density : 300 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 LYS cc_start: 0.7050 (mmmm) cc_final: 0.6493 (pptt) REVERT: A 346 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8157 (t) REVERT: A 419 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7710 (ptm160) REVERT: A 456 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7409 (ttp-110) REVERT: B 658 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: C 69 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7756 (mm) REVERT: C 105 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: D 11 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7275 (tp) REVERT: D 106 VAL cc_start: 0.5744 (OUTLIER) cc_final: 0.5380 (t) REVERT: E 153 GLU cc_start: 0.6748 (tt0) cc_final: 0.6475 (tt0) REVERT: E 168 LYS cc_start: 0.7067 (mmmm) cc_final: 0.6492 (pptt) REVERT: F 535 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7759 (mpt) REVERT: F 658 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: G 30 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8412 (m-10) REVERT: G 80 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8470 (tp) REVERT: H 20 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7329 (mtm180) REVERT: H 79 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.5793 (mp10) REVERT: I 75 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8407 (m) REVERT: I 84 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8448 (mp) REVERT: I 167 ASP cc_start: 0.8175 (m-30) cc_final: 0.7829 (m-30) REVERT: I 168 LYS cc_start: 0.7095 (mmmm) cc_final: 0.6472 (pptt) REVERT: I 205 CYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6497 (m) REVERT: I 360 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8100 (ptt-90) REVERT: J 575 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: J 616 ASN cc_start: 0.8188 (p0) cc_final: 0.7881 (p0) REVERT: J 640 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: J 654 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5421 (tt0) REVERT: K 6 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: K 66 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8052 (ttt90) REVERT: L 78 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6939 (tt) REVERT: L 79 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6151 (mp10) REVERT: M 100 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8421 (mt-10) REVERT: M 100 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.5890 (mmm) REVERT: N 11 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6807 (mm) REVERT: N 50 ASN cc_start: 0.8188 (t0) cc_final: 0.7253 (t0) REVERT: N 85 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6504 (m-30) REVERT: O 97 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.8069 (ttp-170) REVERT: O 100 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: P 37 GLN cc_start: 0.6879 (tt0) cc_final: 0.6653 (tp-100) REVERT: P 50 ASN cc_start: 0.8306 (t0) cc_final: 0.7714 (t0) REVERT: P 85 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6626 (m-30) REVERT: Q 29 MET cc_start: 0.3289 (pmm) cc_final: 0.2980 (pmm) REVERT: R 90 MET cc_start: 0.8632 (tpp) cc_final: 0.8354 (mmt) outliers start: 322 outliers final: 208 residues processed: 568 average time/residue: 1.0985 time to fit residues: 766.5870 Evaluate side-chains 529 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 290 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 44 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 368 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 366 optimal weight: 30.0000 chunk 186 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN M 3 GLN M 99 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.226341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.171404 restraints weight = 33115.021| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 3.71 r_work: 0.3388 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32148 Z= 0.144 Angle : 0.695 10.386 44007 Z= 0.332 Chirality : 0.047 0.304 5334 Planarity : 0.005 0.133 5301 Dihedral : 11.611 156.779 7516 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.03 % Favored : 93.65 % Rotamer: Outliers : 8.85 % Allowed : 31.21 % Favored : 59.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: -1.83 (0.13), residues: 3684 helix: -1.50 (0.24), residues: 435 sheet: -0.70 (0.14), residues: 1284 loop : -1.47 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 610 HIS 0.003 0.001 HIS I 105 PHE 0.012 0.001 PHE I 383 TYR 0.020 0.001 TYR H 140 ARG 0.004 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 63) link_NAG-ASN : angle 2.50260 ( 189) link_ALPHA1-6 : bond 0.00450 ( 15) link_ALPHA1-6 : angle 1.75637 ( 45) link_BETA1-4 : bond 0.00398 ( 51) link_BETA1-4 : angle 1.99339 ( 153) link_ALPHA1-2 : bond 0.00501 ( 15) link_ALPHA1-2 : angle 1.74973 ( 45) link_ALPHA1-3 : bond 0.00731 ( 15) link_ALPHA1-3 : angle 1.47528 ( 45) hydrogen bonds : bond 0.03844 ( 844) hydrogen bonds : angle 5.62925 ( 2367) SS BOND : bond 0.00599 ( 51) SS BOND : angle 2.01136 ( 102) covalent geometry : bond 0.00341 (31938) covalent geometry : angle 0.65598 (43428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 305 time to evaluate : 3.187 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: A 168 LYS cc_start: 0.7176 (mmmm) cc_final: 0.6728 (pptt) REVERT: A 346 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8138 (t) REVERT: A 419 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7709 (ptm160) REVERT: A 456 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7518 (ttp-170) REVERT: B 542 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7124 (ptt90) REVERT: B 658 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: C 179 SER cc_start: 0.7591 (OUTLIER) cc_final: 0.6751 (p) REVERT: D 11 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7239 (tp) REVERT: D 79 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6293 (mp10) REVERT: D 106 VAL cc_start: 0.6231 (OUTLIER) cc_final: 0.5947 (t) REVERT: E 153 GLU cc_start: 0.6732 (tt0) cc_final: 0.6478 (tt0) REVERT: E 168 LYS cc_start: 0.7098 (mmmm) cc_final: 0.6551 (pptt) REVERT: E 228 CYS cc_start: 0.8274 (t) cc_final: 0.8029 (t) REVERT: F 535 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7775 (mpt) REVERT: F 658 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: G 30 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8397 (m-10) REVERT: G 80 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8462 (tp) REVERT: G 94 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7234 (t) REVERT: H 79 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.5849 (mp10) REVERT: I 75 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8388 (m) REVERT: I 84 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8423 (mp) REVERT: I 167 ASP cc_start: 0.8135 (m-30) cc_final: 0.7768 (m-30) REVERT: I 168 LYS cc_start: 0.7144 (mmmm) cc_final: 0.6503 (pptt) REVERT: I 205 CYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6423 (m) REVERT: I 360 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8070 (ptt-90) REVERT: J 575 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: J 616 ASN cc_start: 0.8160 (p0) cc_final: 0.7842 (p0) REVERT: J 640 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: K 66 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8076 (ttt90) REVERT: L 78 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6895 (tt) REVERT: L 79 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.6131 (mp10) REVERT: M 100 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8394 (mt-10) REVERT: M 100 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6587 (mpm) REVERT: N 11 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6802 (mm) REVERT: N 50 ASN cc_start: 0.8270 (t0) cc_final: 0.7232 (t0) REVERT: N 85 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6534 (m-30) REVERT: O 97 ARG cc_start: 0.8305 (ttp-170) cc_final: 0.8040 (ttp-170) REVERT: O 100 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7568 (mt-10) REVERT: P 37 GLN cc_start: 0.7044 (tt0) cc_final: 0.6692 (tp-100) REVERT: P 50 ASN cc_start: 0.8241 (t0) cc_final: 0.7584 (t0) REVERT: P 85 ASP cc_start: 0.6928 (OUTLIER) cc_final: 0.6602 (m-30) REVERT: Q 29 MET cc_start: 0.3200 (pmm) cc_final: 0.2859 (pmm) outliers start: 287 outliers final: 198 residues processed: 547 average time/residue: 1.0722 time to fit residues: 727.2411 Evaluate side-chains 517 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 289 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 0.0970 chunk 330 optimal weight: 40.0000 chunk 215 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 chunk 183 optimal weight: 0.0270 chunk 204 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 185 optimal weight: 0.0770 chunk 248 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 302 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 GLN H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN M 3 GLN M 99 GLN N 51 ASN O 3 GLN O 99 GLN P 51 ASN Q 99 GLN R 37 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.228421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.175643 restraints weight = 33176.762| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.46 r_work: 0.3417 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32148 Z= 0.120 Angle : 0.665 9.599 44007 Z= 0.318 Chirality : 0.046 0.306 5334 Planarity : 0.005 0.130 5301 Dihedral : 11.190 157.859 7504 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.27 % Favored : 94.41 % Rotamer: Outliers : 7.71 % Allowed : 32.35 % Favored : 59.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: -1.67 (0.13), residues: 3684 helix: -1.21 (0.25), residues: 435 sheet: -0.64 (0.14), residues: 1299 loop : -1.37 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 610 HIS 0.003 0.001 HIS I 105 PHE 0.011 0.001 PHE I 383 TYR 0.019 0.001 TYR H 140 ARG 0.004 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 63) link_NAG-ASN : angle 2.42672 ( 189) link_ALPHA1-6 : bond 0.00411 ( 15) link_ALPHA1-6 : angle 1.69970 ( 45) link_BETA1-4 : bond 0.00394 ( 51) link_BETA1-4 : angle 1.89356 ( 153) link_ALPHA1-2 : bond 0.00539 ( 15) link_ALPHA1-2 : angle 1.69326 ( 45) link_ALPHA1-3 : bond 0.00764 ( 15) link_ALPHA1-3 : angle 1.46882 ( 45) hydrogen bonds : bond 0.03475 ( 844) hydrogen bonds : angle 5.42802 ( 2367) SS BOND : bond 0.00715 ( 51) SS BOND : angle 1.82203 ( 102) covalent geometry : bond 0.00276 (31938) covalent geometry : angle 0.62780 (43428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 315 time to evaluate : 3.159 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: A 130 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7787 (mp10) REVERT: A 346 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8109 (t) REVERT: A 419 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7698 (ptm160) REVERT: A 456 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7393 (ttp-170) REVERT: B 640 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8444 (mm-40) REVERT: B 658 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: C 193 THR cc_start: 0.4826 (OUTLIER) cc_final: 0.4585 (p) REVERT: D 11 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7247 (tp) REVERT: D 20 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7848 (mmm160) REVERT: D 79 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6816 (mp10) REVERT: D 106 VAL cc_start: 0.6150 (OUTLIER) cc_final: 0.5900 (t) REVERT: D 143 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5211 (pp20) REVERT: D 166 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7656 (tp40) REVERT: F 535 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7765 (mpt) REVERT: F 658 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: G 80 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8480 (tp) REVERT: G 94 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7215 (t) REVERT: G 193 THR cc_start: 0.4725 (OUTLIER) cc_final: 0.4512 (p) REVERT: H 79 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.5854 (mp10) REVERT: I 75 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8466 (m) REVERT: I 84 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8399 (mp) REVERT: I 167 ASP cc_start: 0.8092 (m-30) cc_final: 0.7792 (m-30) REVERT: I 168 LYS cc_start: 0.7216 (mmmm) cc_final: 0.6568 (pptt) REVERT: J 575 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: J 616 ASN cc_start: 0.8135 (p0) cc_final: 0.7798 (p0) REVERT: J 640 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8303 (mp10) REVERT: K 38 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7207 (ttm-80) REVERT: L 79 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6216 (mp10) REVERT: L 143 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5407 (pp20) REVERT: M 100 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: N 11 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6789 (mm) REVERT: N 50 ASN cc_start: 0.8187 (t0) cc_final: 0.7073 (t0) REVERT: N 85 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6452 (m-30) REVERT: O 97 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7998 (ttp-170) REVERT: O 100 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: P 28 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6580 (mp) REVERT: P 37 GLN cc_start: 0.7048 (tt0) cc_final: 0.6681 (tp-100) REVERT: P 50 ASN cc_start: 0.8204 (t0) cc_final: 0.7402 (t0) REVERT: P 85 ASP cc_start: 0.6902 (OUTLIER) cc_final: 0.6697 (m-30) REVERT: Q 29 MET cc_start: 0.3274 (pmm) cc_final: 0.2934 (pmm) REVERT: R 52 GLN cc_start: 0.7605 (pt0) cc_final: 0.7367 (mt0) outliers start: 250 outliers final: 156 residues processed: 524 average time/residue: 1.1624 time to fit residues: 743.1805 Evaluate side-chains 483 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 297 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 SER Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 290 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 251 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 335 optimal weight: 50.0000 chunk 117 optimal weight: 0.7980 chunk 357 optimal weight: 8.9990 chunk 303 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 356 optimal weight: 0.9980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN D 124 GLN E 103 GLN F 577 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 100 GLN I 130 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN M 3 GLN M 99 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN P 51 ASN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.223744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.169890 restraints weight = 33090.115| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.60 r_work: 0.3329 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3314 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3314 r_free = 0.3314 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3314 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 32148 Z= 0.230 Angle : 0.772 10.422 44007 Z= 0.368 Chirality : 0.050 0.316 5334 Planarity : 0.006 0.129 5301 Dihedral : 11.552 155.891 7486 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.81 % Favored : 92.86 % Rotamer: Outliers : 7.55 % Allowed : 32.50 % Favored : 59.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: -1.81 (0.13), residues: 3684 helix: -1.47 (0.24), residues: 435 sheet: -0.66 (0.14), residues: 1293 loop : -1.49 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP J 610 HIS 0.005 0.001 HIS I 105 PHE 0.015 0.002 PHE E 317 TYR 0.023 0.002 TYR D 140 ARG 0.009 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 63) link_NAG-ASN : angle 2.77029 ( 189) link_ALPHA1-6 : bond 0.00360 ( 15) link_ALPHA1-6 : angle 1.79452 ( 45) link_BETA1-4 : bond 0.00463 ( 51) link_BETA1-4 : angle 2.17736 ( 153) link_ALPHA1-2 : bond 0.00383 ( 15) link_ALPHA1-2 : angle 1.87378 ( 45) link_ALPHA1-3 : bond 0.00620 ( 15) link_ALPHA1-3 : angle 1.43349 ( 45) hydrogen bonds : bond 0.04386 ( 844) hydrogen bonds : angle 5.61748 ( 2367) SS BOND : bond 0.00762 ( 51) SS BOND : angle 2.27482 ( 102) covalent geometry : bond 0.00557 (31938) covalent geometry : angle 0.72982 (43428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 292 time to evaluate : 3.434 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: A 84 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 125 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8280 (mt) REVERT: A 346 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8179 (t) REVERT: A 419 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7805 (ptm160) REVERT: B 621 GLU cc_start: 0.8954 (pt0) cc_final: 0.8661 (pm20) REVERT: B 658 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: C 30 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: C 117 LYS cc_start: 0.7966 (tttm) cc_final: 0.7484 (tmtt) REVERT: C 193 THR cc_start: 0.4807 (OUTLIER) cc_final: 0.4541 (p) REVERT: D 11 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7320 (tp) REVERT: D 20 ARG cc_start: 0.8098 (mmm160) cc_final: 0.7803 (mmm160) REVERT: D 79 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: D 106 VAL cc_start: 0.6006 (OUTLIER) cc_final: 0.5599 (t) REVERT: D 143 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5348 (pp20) REVERT: D 166 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7660 (tp40) REVERT: E 228 CYS cc_start: 0.8369 (t) cc_final: 0.8131 (t) REVERT: F 535 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7770 (mpt) REVERT: F 658 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7469 (tp40) REVERT: G 30 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8407 (m-10) REVERT: G 94 THR cc_start: 0.7973 (OUTLIER) cc_final: 0.7331 (t) REVERT: G 117 LYS cc_start: 0.7972 (tttm) cc_final: 0.7597 (tmtt) REVERT: G 193 THR cc_start: 0.4666 (OUTLIER) cc_final: 0.4442 (p) REVERT: H 79 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.5885 (mp10) REVERT: I 75 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8354 (m) REVERT: I 84 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8492 (mp) REVERT: I 168 LYS cc_start: 0.7249 (mmmm) cc_final: 0.6614 (pptt) REVERT: J 575 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: J 616 ASN cc_start: 0.8182 (p0) cc_final: 0.7790 (p0) REVERT: J 640 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: J 654 GLU cc_start: 0.6156 (OUTLIER) cc_final: 0.5539 (tt0) REVERT: K 38 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7197 (ttm-80) REVERT: L 78 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6792 (tt) REVERT: L 79 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6206 (mp10) REVERT: L 143 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5454 (pp20) REVERT: M 100 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8542 (mt-10) REVERT: N 11 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6818 (mm) REVERT: N 85 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6576 (m-30) REVERT: O 97 ARG cc_start: 0.8327 (ttp-170) cc_final: 0.8039 (ttp-170) REVERT: O 100 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: P 37 GLN cc_start: 0.7054 (tt0) cc_final: 0.6682 (tp-100) REVERT: P 50 ASN cc_start: 0.8119 (t0) cc_final: 0.7416 (t0) REVERT: P 85 ASP cc_start: 0.6791 (OUTLIER) cc_final: 0.6515 (m-30) REVERT: Q 29 MET cc_start: 0.3287 (pmm) cc_final: 0.2964 (pmm) REVERT: R 52 GLN cc_start: 0.7654 (pt0) cc_final: 0.7394 (mt0) outliers start: 245 outliers final: 166 residues processed: 506 average time/residue: 1.2113 time to fit residues: 758.9971 Evaluate side-chains 482 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 284 time to evaluate : 3.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 89 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 249 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 240 optimal weight: 3.9990 chunk 293 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 185 optimal weight: 0.0030 chunk 273 optimal weight: 10.0000 chunk 218 optimal weight: 0.5980 chunk 187 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN B 577 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN E 103 GLN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN G 6 GLN G 105 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN M 3 GLN M 99 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN Q 99 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.228063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.172290 restraints weight = 33249.193| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.81 r_work: 0.3413 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32148 Z= 0.118 Angle : 0.675 10.130 44007 Z= 0.324 Chirality : 0.046 0.305 5334 Planarity : 0.005 0.130 5301 Dihedral : 10.973 157.205 7482 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.18 % Favored : 94.49 % Rotamer: Outliers : 5.92 % Allowed : 34.14 % Favored : 59.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3684 helix: -1.15 (0.25), residues: 435 sheet: -0.61 (0.14), residues: 1308 loop : -1.34 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 34 HIS 0.003 0.001 HIS A 85 PHE 0.012 0.001 PHE L 139 TYR 0.021 0.001 TYR D 140 ARG 0.010 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 63) link_NAG-ASN : angle 2.48303 ( 189) link_ALPHA1-6 : bond 0.00395 ( 15) link_ALPHA1-6 : angle 1.68787 ( 45) link_BETA1-4 : bond 0.00375 ( 51) link_BETA1-4 : angle 1.88203 ( 153) link_ALPHA1-2 : bond 0.00548 ( 15) link_ALPHA1-2 : angle 1.65717 ( 45) link_ALPHA1-3 : bond 0.00748 ( 15) link_ALPHA1-3 : angle 1.43657 ( 45) hydrogen bonds : bond 0.03438 ( 844) hydrogen bonds : angle 5.35982 ( 2367) SS BOND : bond 0.00517 ( 51) SS BOND : angle 1.85485 ( 102) covalent geometry : bond 0.00272 (31938) covalent geometry : angle 0.63776 (43428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7368 Ramachandran restraints generated. 3684 Oldfield, 0 Emsley, 3684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 307 time to evaluate : 3.090 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: A 130 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7794 (mp10) REVERT: A 167 ASP cc_start: 0.8157 (m-30) cc_final: 0.7843 (m-30) REVERT: A 346 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8145 (t) REVERT: B 621 GLU cc_start: 0.8847 (pt0) cc_final: 0.8562 (pm20) REVERT: B 640 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8379 (mm-40) REVERT: C 105 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: D 11 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7279 (tp) REVERT: D 20 ARG cc_start: 0.8120 (mmm160) cc_final: 0.7907 (mmm160) REVERT: D 79 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: D 143 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5247 (pp20) REVERT: D 166 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7777 (tp40) REVERT: F 535 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7749 (mpt) REVERT: F 658 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: G 80 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8504 (tp) REVERT: G 94 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7238 (t) REVERT: G 105 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: G 117 LYS cc_start: 0.8048 (tttm) cc_final: 0.7681 (tmtt) REVERT: H 79 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.5988 (mp10) REVERT: I 75 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8466 (m) REVERT: I 84 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8413 (mp) REVERT: I 168 LYS cc_start: 0.7157 (mmmm) cc_final: 0.6562 (pptt) REVERT: J 575 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: J 616 ASN cc_start: 0.8127 (p0) cc_final: 0.7757 (p0) REVERT: J 640 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8304 (mp10) REVERT: K 38 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7158 (ttm-80) REVERT: L 79 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6434 (mp10) REVERT: L 143 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5382 (pp20) REVERT: N 11 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6753 (mm) REVERT: N 85 ASP cc_start: 0.7020 (OUTLIER) cc_final: 0.6730 (m-30) REVERT: O 97 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.8038 (ttp-170) REVERT: O 100 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: P 37 GLN cc_start: 0.7145 (tt0) cc_final: 0.6884 (tp-100) REVERT: P 50 ASN cc_start: 0.8116 (t0) cc_final: 0.7361 (t0) REVERT: P 90 MET cc_start: 0.8601 (tpp) cc_final: 0.8342 (mmt) REVERT: R 52 GLN cc_start: 0.7657 (pt0) cc_final: 0.7449 (mt0) outliers start: 192 outliers final: 140 residues processed: 470 average time/residue: 1.1686 time to fit residues: 667.2985 Evaluate side-chains 461 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 298 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 166 GLN Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 432 GLN Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 446 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 75 LYS Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 100 SER Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 180 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN B 575 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN D 124 GLN E 103 GLN F 616 ASN G 6 GLN G 105 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 124 GLN M 3 GLN M 99 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN Q 99 GLN R 51 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.226749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.173635 restraints weight = 32968.757| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.54 r_work: 0.3388 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32148 Z= 0.155 Angle : 0.705 11.774 44007 Z= 0.337 Chirality : 0.047 0.306 5334 Planarity : 0.005 0.131 5301 Dihedral : 10.949 157.112 7469 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.03 % Favored : 93.65 % Rotamer: Outliers : 6.41 % Allowed : 33.70 % Favored : 59.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3684 helix: -1.19 (0.25), residues: 435 sheet: -0.58 (0.14), residues: 1296 loop : -1.35 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 610 HIS 0.003 0.001 HIS E 105 PHE 0.012 0.001 PHE A 383 TYR 0.037 0.001 TYR N 87 ARG 0.014 0.000 ARG A 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 63) link_NAG-ASN : angle 2.52881 ( 189) link_ALPHA1-6 : bond 0.00379 ( 15) link_ALPHA1-6 : angle 1.70890 ( 45) link_BETA1-4 : bond 0.00412 ( 51) link_BETA1-4 : angle 1.98859 ( 153) link_ALPHA1-2 : bond 0.00475 ( 15) link_ALPHA1-2 : angle 1.74043 ( 45) link_ALPHA1-3 : bond 0.00702 ( 15) link_ALPHA1-3 : angle 1.44375 ( 45) hydrogen bonds : bond 0.03735 ( 844) hydrogen bonds : angle 5.35124 ( 2367) SS BOND : bond 0.00609 ( 51) SS BOND : angle 1.94805 ( 102) covalent geometry : bond 0.00368 (31938) covalent geometry : angle 0.66723 (43428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23884.70 seconds wall clock time: 412 minutes 14.48 seconds (24734.48 seconds total)