Starting phenix.real_space_refine on Fri Jun 27 00:09:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ttw_41613/06_2025/8ttw_41613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ttw_41613/06_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_41613/06_2025/8ttw_41613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ttw_41613/06_2025/8ttw_41613.map" model { file = "/net/cci-nas-00/data/ceres_data/8ttw_41613/06_2025/8ttw_41613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ttw_41613/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 17.98, per 1000 atoms: 0.57 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: 9.23 Conformation dependent library (CDL) restraints added in 3.6 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: 4.47 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: 12.79 Time building geometry restraints manager: 10.69 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: 3.160 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: 1.300 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 71.910 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.370 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: 0.020 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.140 ------------------------------------------------------------------------------- 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 : 3.437 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: 1.1343 time to fit residues: 903.9226 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 : 3.370 ------------------------------------------------------------------------------- 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: 0.3281 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 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 = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 3.656 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: 0.8741 (OUTLIER) cc_final: 0.8352 (mt) REVERT: A 325 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8306 (p0) REVERT: A 358 ILE cc_start: 0.8170 (pt) cc_final: 0.7957 (pp) REVERT: A 419 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7811 (ptm160) REVERT: A 456 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7662 (ttp-170) REVERT: C 30 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8432 (m-10) REVERT: D 11 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7161 (tp) REVERT: E 153 GLU cc_start: 0.7006 (tt0) cc_final: 0.6600 (pt0) REVERT: E 456 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7634 (mtp180) REVERT: F 535 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7496 (mmt) REVERT: F 624 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8051 (p0) REVERT: G 30 PHE cc_start: 0.9011 (OUTLIER) cc_final: 0.8431 (m-10) REVERT: G 80 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8473 (tp) REVERT: G 100 ASP cc_start: 0.7743 (t0) cc_final: 0.7493 (m-30) REVERT: H 61 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.6498 (ptt-90) REVERT: H 79 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.5777 (mp10) REVERT: I 100 MET cc_start: 0.8913 (mtp) cc_final: 0.8659 (mtp) REVERT: I 189 LYS cc_start: 0.7782 (OUTLIER) cc_final: 0.6424 (tmtt) REVERT: I 360 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8214 (ptt-90) REVERT: J 575 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8165 (tp-100) REVERT: J 640 GLN cc_start: 0.8720 (OUTLIER) cc_final: 0.8340 (mp10) REVERT: J 654 GLU cc_start: 0.6365 (OUTLIER) cc_final: 0.5833 (tt0) REVERT: K 13 LYS cc_start: 0.8190 (mmpt) cc_final: 0.7819 (mmtt) REVERT: L 61 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6612 (ptt-90) REVERT: L 79 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.5831 (mp10) REVERT: M 77 GLN cc_start: 0.6829 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: N 11 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6780 (mm) REVERT: N 50 ASN cc_start: 0.8177 (t0) cc_final: 0.7444 (t0) REVERT: O 29 MET cc_start: 0.3668 (OUTLIER) cc_final: 0.3413 (pmt) REVERT: O 77 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.6226 (pm20) REVERT: P 28 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6670 (mp) REVERT: P 50 ASN cc_start: 0.8117 (t0) cc_final: 0.7613 (t0) REVERT: Q 77 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.6182 (pm20) outliers start: 440 outliers final: 263 residues processed: 701 average time/residue: 1.1051 time to fit residues: 950.7248 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 : 3.132 ------------------------------------------------------------------------------- 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: 9.9990 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: 2.9990 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: 2.3788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.222633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.167609 restraints weight = 33238.580| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.89 r_work: 0.3305 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1373 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= 0.240 Angle : 0.808 11.313 44007 Z= 0.389 Chirality : 0.051 0.291 5334 Planarity : 0.006 0.138 5301 Dihedral : 14.056 155.245 7660 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.73 % Favored : 92.83 % Rotamer: Outliers : 12.18 % Allowed : 28.12 % Favored : 59.70 % 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: -2.23 (0.13), residues: 3684 helix: -2.37 (0.22), residues: 435 sheet: -0.93 (0.14), residues: 1281 loop : -1.61 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 610 HIS 0.005 0.001 HIS I 105 PHE 0.013 0.002 PHE G 91 TYR 0.032 0.002 TYR H 140 ARG 0.009 0.000 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00531 ( 63) link_NAG-ASN : angle 2.78187 ( 189) link_ALPHA1-6 : bond 0.00363 ( 15) link_ALPHA1-6 : angle 1.96105 ( 45) link_BETA1-4 : bond 0.00411 ( 51) link_BETA1-4 : angle 2.19692 ( 153) link_ALPHA1-2 : bond 0.00441 ( 15) link_ALPHA1-2 : angle 1.88684 ( 45) link_ALPHA1-3 : bond 0.00662 ( 15) link_ALPHA1-3 : angle 1.54132 ( 45) hydrogen bonds : bond 0.05204 ( 844) hydrogen bonds : angle 6.63058 ( 2367) SS BOND : bond 0.00776 ( 51) SS BOND : angle 2.38084 ( 102) covalent geometry : bond 0.00577 (31938) covalent geometry : angle 0.76650 (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 714 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 395 poor density : 319 time to evaluate : 3.271 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: 0.8686 (OUTLIER) cc_final: 0.8293 (mt) REVERT: A 155 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.7797 (mmmt) REVERT: A 456 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7572 (ttp-110) REVERT: B 658 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: C 30 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8409 (m-10) REVERT: D 11 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7333 (tp) REVERT: E 153 GLU cc_start: 0.6933 (tt0) cc_final: 0.6478 (pt0) REVERT: F 535 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7606 (mmt) REVERT: F 616 ASN cc_start: 0.8343 (p0) cc_final: 0.8015 (p0) REVERT: F 624 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7982 (p0) REVERT: F 658 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7541 (tt0) REVERT: G 30 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8434 (m-10) REVERT: G 100 ASP cc_start: 0.7689 (t0) cc_final: 0.7477 (m-30) REVERT: G 105 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8083 (pt0) REVERT: G 179 SER cc_start: 0.7368 (OUTLIER) cc_final: 0.6557 (p) REVERT: H 61 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6506 (ptt-90) REVERT: H 79 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.5769 (mp10) REVERT: I 84 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8476 (mp) REVERT: I 189 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.6421 (tmtt) REVERT: I 268 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7451 (mt-10) REVERT: I 360 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8175 (ptt-90) REVERT: J 568 LEU cc_start: 0.7515 (tp) cc_final: 0.7264 (tp) REVERT: J 575 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8083 (tp-100) REVERT: J 640 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8270 (mp10) REVERT: J 654 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5614 (tt0) REVERT: L 61 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6539 (ptt-90) REVERT: L 72 THR cc_start: 0.7939 (p) cc_final: 0.7734 (t) REVERT: L 78 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7143 (tt) REVERT: L 79 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.6124 (mp10) REVERT: N 11 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6681 (mm) REVERT: N 50 ASN cc_start: 0.8174 (t0) cc_final: 0.7293 (t0) REVERT: O 29 MET cc_start: 0.3567 (OUTLIER) cc_final: 0.3310 (pmt) REVERT: P 28 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6680 (mp) REVERT: P 50 ASN cc_start: 0.8231 (t0) cc_final: 0.7611 (t0) outliers start: 395 outliers final: 246 residues processed: 646 average time/residue: 1.1652 time to fit residues: 928.1158 Evaluate side-chains 579 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 307 time to evaluate : 3.232 ------------------------------------------------------------------------------- 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 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 155 LYS 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 649 SER 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 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 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 51 THR 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 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 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 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 658 GLN 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 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 97 THR Chi-restraints excluded: chain H residue 106 VAL 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 51 THR 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 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 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 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 649 SER 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 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 7 SER Chi-restraints excluded: chain L residue 30 THR 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 66 ARG 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 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 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 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 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: 5.9990 chunk 57 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 111 optimal weight: 0.0270 chunk 321 optimal weight: 9.9990 chunk 310 optimal weight: 4.9990 chunk 309 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 332 optimal weight: 20.0000 chunk 367 optimal weight: 2.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- 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 H 100 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.223064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.169390 restraints weight = 33223.398| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.52 r_work: 0.3333 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 32148 Z= 0.208 Angle : 0.781 12.793 44007 Z= 0.372 Chirality : 0.050 0.299 5334 Planarity : 0.006 0.143 5301 Dihedral : 13.284 155.543 7614 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.14 % Favored : 92.45 % Rotamer: Outliers : 11.66 % Allowed : 28.31 % 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: -2.15 (0.13), residues: 3684 helix: -2.13 (0.23), residues: 435 sheet: -0.89 (0.14), residues: 1299 loop : -1.59 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 610 HIS 0.004 0.001 HIS I 105 PHE 0.013 0.002 PHE G 91 TYR 0.026 0.002 TYR H 140 ARG 0.006 0.000 ARG E 500 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 63) link_NAG-ASN : angle 2.71404 ( 189) link_ALPHA1-6 : bond 0.00372 ( 15) link_ALPHA1-6 : angle 1.92362 ( 45) link_BETA1-4 : bond 0.00392 ( 51) link_BETA1-4 : angle 2.14555 ( 153) link_ALPHA1-2 : bond 0.00448 ( 15) link_ALPHA1-2 : angle 1.86601 ( 45) link_ALPHA1-3 : bond 0.00675 ( 15) link_ALPHA1-3 : angle 1.56071 ( 45) hydrogen bonds : bond 0.04639 ( 844) hydrogen bonds : angle 6.25475 ( 2367) SS BOND : bond 0.00888 ( 51) SS BOND : angle 2.31924 ( 102) covalent geometry : bond 0.00500 (31938) covalent geometry : angle 0.73936 (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 691 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 378 poor density : 313 time to evaluate : 3.073 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: A 125 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8280 (mt) REVERT: A 346 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8213 (t) REVERT: A 419 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7724 (ptm160) REVERT: A 456 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7533 (ttp-110) REVERT: C 30 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8430 (m-10) REVERT: C 179 SER cc_start: 0.7692 (OUTLIER) cc_final: 0.6824 (p) REVERT: D 11 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7330 (tp) REVERT: D 20 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7750 (mmm160) REVERT: D 166 GLN cc_start: 0.7658 (tt0) cc_final: 0.7160 (tp40) REVERT: E 153 GLU cc_start: 0.6913 (tt0) cc_final: 0.6455 (pt0) REVERT: F 535 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7798 (mpt) REVERT: F 542 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7553 (ptt90) REVERT: F 624 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7967 (p0) REVERT: F 658 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: G 30 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8432 (m-10) REVERT: G 80 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8493 (tp) REVERT: G 100 ASP cc_start: 0.7633 (t0) cc_final: 0.7433 (m-30) REVERT: G 105 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: H 20 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7254 (mtm180) REVERT: H 61 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6487 (ptt-90) REVERT: H 79 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.5745 (mp10) REVERT: I 75 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8408 (m) REVERT: I 84 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8472 (mp) REVERT: I 189 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.6430 (tmtt) REVERT: I 268 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7589 (mt-10) REVERT: I 360 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8162 (ptt-90) REVERT: J 575 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8027 (tp-100) REVERT: J 616 ASN cc_start: 0.8294 (p0) cc_final: 0.7968 (p0) REVERT: J 640 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: J 654 GLU cc_start: 0.6197 (OUTLIER) cc_final: 0.5551 (tt0) REVERT: K 66 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8135 (ttt90) REVERT: L 61 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6680 (ptt-90) REVERT: L 78 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7261 (tt) REVERT: L 79 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.6145 (mp10) REVERT: L 107 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.6240 (tptt) REVERT: M 100 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: M 100 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.5975 (mmm) REVERT: N 11 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6804 (mm) REVERT: N 50 ASN cc_start: 0.8227 (t0) cc_final: 0.7304 (t0) REVERT: O 82 VAL cc_start: 0.3899 (OUTLIER) cc_final: 0.3244 (t) REVERT: P 50 ASN cc_start: 0.8369 (t0) cc_final: 0.7744 (t0) outliers start: 378 outliers final: 235 residues processed: 622 average time/residue: 1.1744 time to fit residues: 892.9025 Evaluate side-chains 575 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 307 time to evaluate : 3.182 ------------------------------------------------------------------------------- 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 106 THR 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 161 MET 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 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 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 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 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 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 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 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 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 476 ARG Chi-restraints excluded: chain E residue 499 THR 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 624 ASP Chi-restraints excluded: chain F residue 635 ILE 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 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 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 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 72 THR Chi-restraints excluded: chain H residue 79 GLN 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 51 THR 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 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 356 ASN 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 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 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 172 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 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 105 GLU 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 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 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 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 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 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 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 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: 0.7980 chunk 301 optimal weight: 30.0000 chunk 175 optimal weight: 20.0000 chunk 144 optimal weight: 0.0270 chunk 26 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 365 optimal weight: 4.9990 chunk 363 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 38 optimal weight: 0.0970 overall best weight: 1.9840 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.223716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.170347 restraints weight = 33019.647| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.59 r_work: 0.3324 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32148 Z= 0.209 Angle : 0.769 12.350 44007 Z= 0.366 Chirality : 0.049 0.300 5334 Planarity : 0.006 0.140 5301 Dihedral : 12.798 155.636 7573 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.87 % Favored : 92.75 % Rotamer: Outliers : 11.22 % Allowed : 28.65 % Favored : 60.13 % 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: -2.11 (0.13), residues: 3684 helix: -1.99 (0.23), residues: 435 sheet: -0.89 (0.14), residues: 1305 loop : -1.58 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 610 HIS 0.004 0.001 HIS I 105 PHE 0.014 0.002 PHE G 91 TYR 0.023 0.002 TYR H 140 ARG 0.005 0.000 ARG A 429 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 63) link_NAG-ASN : angle 2.68763 ( 189) link_ALPHA1-6 : bond 0.00409 ( 15) link_ALPHA1-6 : angle 1.96146 ( 45) link_BETA1-4 : bond 0.00421 ( 51) link_BETA1-4 : angle 2.15090 ( 153) link_ALPHA1-2 : bond 0.00434 ( 15) link_ALPHA1-2 : angle 1.86880 ( 45) link_ALPHA1-3 : bond 0.00677 ( 15) link_ALPHA1-3 : angle 1.54737 ( 45) hydrogen bonds : bond 0.04504 ( 844) hydrogen bonds : angle 6.04405 ( 2367) SS BOND : bond 0.00636 ( 51) SS BOND : angle 2.18276 ( 102) covalent geometry : bond 0.00502 (31938) covalent geometry : angle 0.72851 (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 672 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 364 poor density : 308 time to evaluate : 3.605 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 84 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 125 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8272 (mt) REVERT: A 168 LYS cc_start: 0.7107 (mmmm) cc_final: 0.6560 (pptt) REVERT: A 419 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7753 (ptm160) REVERT: A 456 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7689 (ttp-170) REVERT: B 658 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: C 30 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8427 (m-10) REVERT: C 69 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7886 (mm) REVERT: D 11 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7318 (tp) REVERT: D 106 VAL cc_start: 0.6333 (OUTLIER) cc_final: 0.5960 (t) REVERT: E 150 MET cc_start: 0.3655 (tmt) cc_final: 0.3445 (tmt) REVERT: E 153 GLU cc_start: 0.6890 (tt0) cc_final: 0.6402 (pt0) REVERT: F 535 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7795 (mpt) REVERT: F 542 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7542 (ptt90) REVERT: F 658 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7469 (tp40) REVERT: G 30 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8438 (m-10) REVERT: G 80 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8483 (tp) REVERT: G 100 ASP cc_start: 0.7666 (t0) cc_final: 0.7443 (m-30) REVERT: H 20 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7315 (mtm180) REVERT: H 61 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6381 (ptt-90) REVERT: H 79 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.5749 (mp10) REVERT: I 75 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8408 (m) REVERT: I 84 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8471 (mp) REVERT: I 360 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8156 (ptt-90) REVERT: J 575 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8047 (tp-100) REVERT: J 616 ASN cc_start: 0.8314 (p0) cc_final: 0.7993 (p0) REVERT: J 640 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8222 (mp10) REVERT: J 654 GLU cc_start: 0.6144 (OUTLIER) cc_final: 0.5500 (tt0) REVERT: K 66 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8121 (ttt90) REVERT: L 79 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.6223 (mp10) REVERT: L 143 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5289 (tm-30) REVERT: M 100 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: M 100 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.5898 (mmm) REVERT: N 11 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6775 (mm) REVERT: N 50 ASN cc_start: 0.8233 (t0) cc_final: 0.7251 (t0) REVERT: N 90 MET cc_start: 0.8536 (tpp) cc_final: 0.8298 (mmt) REVERT: O 97 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.8194 (ttp-170) REVERT: O 100 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: P 50 ASN cc_start: 0.8328 (t0) cc_final: 0.7650 (t0) REVERT: P 79 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.5317 (pp20) REVERT: R 90 MET cc_start: 0.8714 (tpp) cc_final: 0.8351 (mmt) outliers start: 364 outliers final: 238 residues processed: 611 average time/residue: 1.2259 time to fit residues: 919.1998 Evaluate side-chains 570 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 301 time to evaluate : 3.252 ------------------------------------------------------------------------------- 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 84 ILE 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 161 MET 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 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 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 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 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 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 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 51 THR 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 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 E residue 476 ARG 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 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 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 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 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 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 201 ILE 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 356 ASN 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 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 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 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 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 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 4 LEU 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 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 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 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 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: 0.6980 chunk 331 optimal weight: 10.0000 chunk 4 optimal weight: 0.0370 chunk 81 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 349 optimal weight: 6.9990 chunk 364 optimal weight: 6.9990 overall best weight: 1.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN D 3 GLN D 124 GLN D 166 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 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 O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.225151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.170754 restraints weight = 33211.002| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 3.71 r_work: 0.3355 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32148 Z= 0.163 Angle : 0.726 11.414 44007 Z= 0.346 Chirality : 0.048 0.303 5334 Planarity : 0.005 0.137 5301 Dihedral : 12.126 156.098 7548 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.38 % Favored : 93.30 % Rotamer: Outliers : 10.24 % Allowed : 29.60 % Favored : 60.16 % 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: -1.99 (0.13), residues: 3684 helix: -1.78 (0.24), residues: 435 sheet: -0.78 (0.14), residues: 1263 loop : -1.55 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 610 HIS 0.003 0.001 HIS I 105 PHE 0.012 0.001 PHE I 383 TYR 0.021 0.001 TYR H 140 ARG 0.004 0.000 ARG P 70 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 63) link_NAG-ASN : angle 2.59361 ( 189) link_ALPHA1-6 : bond 0.00464 ( 15) link_ALPHA1-6 : angle 1.91376 ( 45) link_BETA1-4 : bond 0.00394 ( 51) link_BETA1-4 : angle 2.04903 ( 153) link_ALPHA1-2 : bond 0.00494 ( 15) link_ALPHA1-2 : angle 1.79826 ( 45) link_ALPHA1-3 : bond 0.00729 ( 15) link_ALPHA1-3 : angle 1.52304 ( 45) hydrogen bonds : bond 0.04079 ( 844) hydrogen bonds : angle 5.82097 ( 2367) SS BOND : bond 0.00594 ( 51) SS BOND : angle 2.05441 ( 102) covalent geometry : bond 0.00391 (31938) covalent geometry : angle 0.68563 (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 644 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 332 poor density : 312 time to evaluate : 3.549 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: 0.8843 (OUTLIER) cc_final: 0.8566 (mp) REVERT: A 125 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8245 (mt) REVERT: A 168 LYS cc_start: 0.7062 (mmmm) cc_final: 0.6510 (pptt) REVERT: A 346 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8167 (t) REVERT: A 419 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7707 (ptm160) REVERT: A 456 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7633 (ttp-170) REVERT: B 658 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: C 6 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8137 (mt0) REVERT: C 69 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7741 (mm) REVERT: C 105 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7955 (pm20) REVERT: C 179 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.6819 (p) REVERT: D 11 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7289 (tp) REVERT: D 79 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6291 (mp10) REVERT: D 106 VAL cc_start: 0.5780 (OUTLIER) cc_final: 0.5405 (t) REVERT: E 153 GLU cc_start: 0.6775 (tt0) cc_final: 0.6450 (tt0) REVERT: E 168 LYS cc_start: 0.7097 (mmmm) cc_final: 0.6514 (pptt) REVERT: F 535 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7771 (mpt) REVERT: F 658 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7387 (tp40) REVERT: G 30 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8417 (m-10) REVERT: G 80 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8460 (tp) REVERT: H 20 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7342 (mtm180) REVERT: H 79 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.5786 (mp10) REVERT: I 75 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8396 (m) REVERT: I 84 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8438 (mp) REVERT: I 167 ASP cc_start: 0.8217 (m-30) cc_final: 0.7875 (m-30) REVERT: I 168 LYS cc_start: 0.7085 (mmmm) cc_final: 0.6490 (pptt) REVERT: I 360 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8123 (ptt-90) REVERT: J 568 LEU cc_start: 0.7487 (tp) cc_final: 0.7280 (tp) REVERT: J 575 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: J 616 ASN cc_start: 0.8266 (p0) cc_final: 0.7931 (p0) REVERT: J 640 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: J 654 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5415 (tt0) REVERT: K 6 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: K 66 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8094 (ttt90) REVERT: L 79 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6094 (mp10) REVERT: L 143 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.5548 (pp20) REVERT: M 100 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: N 11 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6794 (mm) REVERT: N 50 ASN cc_start: 0.8162 (t0) cc_final: 0.7240 (t0) REVERT: N 85 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: N 90 MET cc_start: 0.8459 (tpp) cc_final: 0.8245 (mmt) REVERT: O 97 ARG cc_start: 0.8335 (ttp-170) cc_final: 0.8083 (ttp-170) REVERT: O 100 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: P 28 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6523 (mp) REVERT: P 37 GLN cc_start: 0.6899 (tt0) cc_final: 0.6674 (tp-100) REVERT: P 50 ASN cc_start: 0.8304 (t0) cc_final: 0.7641 (t0) REVERT: Q 29 MET cc_start: 0.3334 (OUTLIER) cc_final: 0.2994 (pmm) REVERT: R 90 MET cc_start: 0.8606 (tpp) cc_final: 0.8300 (mmt) outliers start: 332 outliers final: 210 residues processed: 583 average time/residue: 1.1249 time to fit residues: 805.4997 Evaluate side-chains 542 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 297 time to evaluate : 3.359 ------------------------------------------------------------------------------- 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 47 ASP 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 84 ILE 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 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 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 604 CYS 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 6 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 78 VAL Chi-restraints excluded: chain P residue 85 ASP Chi-restraints excluded: chain Q residue 29 MET 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 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 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: 0.6980 chunk 67 optimal weight: 2.9990 chunk 368 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 168 optimal weight: 0.0870 chunk 30 optimal weight: 0.8980 chunk 96 optimal weight: 30.0000 chunk 180 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 366 optimal weight: 30.0000 chunk 186 optimal weight: 0.8980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 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 R 37 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.226640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.174593 restraints weight = 33137.957| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.46 r_work: 0.3397 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- 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 = 0.64 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: 0.8255 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32148 Z= 0.137 Angle : 0.691 10.613 44007 Z= 0.330 Chirality : 0.047 0.305 5334 Planarity : 0.005 0.134 5301 Dihedral : 11.630 156.843 7521 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.00 % Favored : 93.68 % Rotamer: Outliers : 8.82 % Allowed : 31.14 % Favored : 60.04 % 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: -1.86 (0.13), residues: 3684 helix: -1.51 (0.24), residues: 435 sheet: -0.74 (0.14), residues: 1287 loop : -1.48 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 610 HIS 0.003 0.001 HIS E 105 PHE 0.012 0.001 PHE I 383 TYR 0.019 0.001 TYR H 140 ARG 0.004 0.000 ARG A 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 63) link_NAG-ASN : angle 2.50546 ( 189) link_ALPHA1-6 : bond 0.00464 ( 15) link_ALPHA1-6 : angle 1.74064 ( 45) link_BETA1-4 : bond 0.00401 ( 51) link_BETA1-4 : angle 1.97827 ( 153) link_ALPHA1-2 : bond 0.00509 ( 15) link_ALPHA1-2 : angle 1.74316 ( 45) link_ALPHA1-3 : bond 0.00746 ( 15) link_ALPHA1-3 : angle 1.48144 ( 45) hydrogen bonds : bond 0.03792 ( 844) hydrogen bonds : angle 5.64132 ( 2367) SS BOND : bond 0.00548 ( 51) SS BOND : angle 1.91556 ( 102) covalent geometry : bond 0.00323 (31938) covalent geometry : angle 0.65202 (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 591 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 286 poor density : 305 time to evaluate : 3.220 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 125 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8204 (mt) REVERT: A 168 LYS cc_start: 0.7192 (mmmm) cc_final: 0.6785 (pptt) REVERT: A 346 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8152 (t) REVERT: A 419 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7706 (ptm160) REVERT: A 456 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7564 (ttp-170) REVERT: B 658 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: D 11 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7279 (tp) REVERT: D 79 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6574 (mp10) REVERT: D 106 VAL cc_start: 0.6229 (OUTLIER) cc_final: 0.5953 (t) REVERT: E 153 GLU cc_start: 0.6736 (tt0) cc_final: 0.6514 (tt0) REVERT: E 168 LYS cc_start: 0.7121 (mmmm) cc_final: 0.6601 (pptt) REVERT: E 228 CYS cc_start: 0.8273 (t) cc_final: 0.8028 (t) REVERT: F 535 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7716 (mpt) REVERT: F 658 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: G 30 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: G 80 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (tp) REVERT: G 105 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7526 (pt0) REVERT: H 79 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.5943 (mp10) REVERT: I 75 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8449 (m) REVERT: I 84 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8444 (mp) REVERT: I 168 LYS cc_start: 0.7087 (mmmm) cc_final: 0.6523 (pptt) REVERT: I 205 CYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6460 (m) REVERT: I 360 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8022 (ptt-90) REVERT: J 575 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: J 616 ASN cc_start: 0.8212 (p0) cc_final: 0.7879 (p0) REVERT: J 640 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8277 (mp10) REVERT: K 66 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8145 (ttt90) REVERT: L 79 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6177 (mp10) REVERT: M 100 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: M 100 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.5920 (mmm) REVERT: N 11 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6825 (mm) REVERT: N 50 ASN cc_start: 0.8329 (t0) cc_final: 0.7288 (t0) REVERT: N 85 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6579 (m-30) REVERT: O 97 ARG cc_start: 0.8409 (ttp-170) cc_final: 0.8184 (ttp-170) REVERT: O 100 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: P 28 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6596 (mp) REVERT: P 37 GLN cc_start: 0.7186 (tt0) cc_final: 0.6849 (tp-100) REVERT: P 50 ASN cc_start: 0.8323 (t0) cc_final: 0.7687 (t0) REVERT: P 85 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: Q 29 MET cc_start: 0.3260 (pmm) cc_final: 0.2937 (pmm) REVERT: R 90 MET cc_start: 0.8548 (tpp) cc_final: 0.8283 (mmt) outliers start: 286 outliers final: 183 residues processed: 545 average time/residue: 1.1276 time to fit residues: 759.4617 Evaluate side-chains 502 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 290 time to evaluate : 3.067 ------------------------------------------------------------------------------- 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 47 ASP 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 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 393 SER 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 658 GLN 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 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 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 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 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 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 105 GLN 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 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 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 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 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 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 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 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 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 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 28 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 330 optimal weight: 40.0000 chunk 215 optimal weight: 0.9990 chunk 254 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 204 optimal weight: 6.9990 chunk 110 optimal weight: 0.0060 chunk 185 optimal weight: 0.0770 chunk 248 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN C 6 GLN 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 105 GLN G 171 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 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.228713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.176023 restraints weight = 33198.056| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.46 r_work: 0.3422 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32148 Z= 0.118 Angle : 0.666 10.102 44007 Z= 0.318 Chirality : 0.046 0.306 5334 Planarity : 0.005 0.131 5301 Dihedral : 11.171 157.924 7497 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.40 % Favored : 94.27 % Rotamer: Outliers : 7.31 % Allowed : 32.69 % Favored : 60.01 % 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: -1.68 (0.13), residues: 3684 helix: -1.19 (0.25), residues: 435 sheet: -0.66 (0.14), residues: 1299 loop : -1.38 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 610 HIS 0.003 0.001 HIS E 105 PHE 0.011 0.001 PHE I 383 TYR 0.024 0.001 TYR D 140 ARG 0.004 0.000 ARG D 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 63) link_NAG-ASN : angle 2.48328 ( 189) link_ALPHA1-6 : bond 0.00418 ( 15) link_ALPHA1-6 : angle 1.69956 ( 45) link_BETA1-4 : bond 0.00397 ( 51) link_BETA1-4 : angle 1.88742 ( 153) link_ALPHA1-2 : bond 0.00537 ( 15) link_ALPHA1-2 : angle 1.68458 ( 45) link_ALPHA1-3 : bond 0.00750 ( 15) link_ALPHA1-3 : angle 1.47409 ( 45) hydrogen bonds : bond 0.03441 ( 844) hydrogen bonds : angle 5.42219 ( 2367) SS BOND : bond 0.00522 ( 51) SS BOND : angle 1.79088 ( 102) covalent geometry : bond 0.00272 (31938) covalent geometry : angle 0.62778 (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 555 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 318 time to evaluate : 3.157 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: 0.8437 (mm-40) cc_final: 0.7801 (mp10) REVERT: A 346 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8106 (t) REVERT: A 456 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7395 (ttp-170) REVERT: B 640 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8423 (mm-40) REVERT: B 658 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7474 (tp40) REVERT: C 193 THR cc_start: 0.4780 (OUTLIER) cc_final: 0.4556 (p) REVERT: D 11 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7248 (tp) REVERT: D 20 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7897 (mmm160) REVERT: D 79 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6852 (mp10) REVERT: D 106 VAL cc_start: 0.5940 (OUTLIER) cc_final: 0.5591 (t) REVERT: D 143 GLU cc_start: 0.6088 (OUTLIER) cc_final: 0.5335 (pp20) REVERT: D 166 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7580 (tp40) REVERT: F 535 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7750 (mpt) REVERT: F 658 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: G 80 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8504 (tp) REVERT: G 94 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7165 (t) REVERT: G 117 LYS cc_start: 0.7973 (tttm) cc_final: 0.7598 (tmtt) REVERT: G 193 THR cc_start: 0.4668 (OUTLIER) cc_final: 0.4460 (p) REVERT: H 79 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.5897 (mp10) REVERT: I 75 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8454 (m) REVERT: I 84 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8402 (mp) REVERT: I 167 ASP cc_start: 0.8033 (m-30) cc_final: 0.7782 (m-30) REVERT: I 168 LYS cc_start: 0.7088 (mmmm) cc_final: 0.6527 (pptt) REVERT: I 205 CYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6433 (m) REVERT: J 575 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: J 616 ASN cc_start: 0.8199 (p0) cc_final: 0.7873 (p0) REVERT: J 640 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: K 38 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7220 (ttm-80) REVERT: L 79 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6249 (mp10) REVERT: L 143 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5436 (pp20) REVERT: M 100 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: M 100 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.5777 (mmm) REVERT: N 11 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6796 (mm) REVERT: N 50 ASN cc_start: 0.8150 (t0) cc_final: 0.7525 (t0) REVERT: N 85 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6451 (m-30) REVERT: O 97 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.8051 (ttp-170) REVERT: O 100 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: P 37 GLN cc_start: 0.7008 (tt0) cc_final: 0.6715 (tp-100) REVERT: P 50 ASN cc_start: 0.8220 (t0) cc_final: 0.7497 (t0) REVERT: Q 29 MET cc_start: 0.3254 (pmm) cc_final: 0.2919 (pmm) outliers start: 237 outliers final: 149 residues processed: 517 average time/residue: 1.1900 time to fit residues: 753.3171 Evaluate side-chains 485 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 307 time to evaluate : 3.155 ------------------------------------------------------------------------------- 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 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 456 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 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 107 LYS 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 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 426 MET Chi-restraints excluded: chain E residue 447 SER 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 624 ASP 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 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 106 VAL 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 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 371 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 415 THR 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 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 184 VAL Chi-restraints excluded: chain L residue 7 SER 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 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 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 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 68 VAL 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 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: 10.0000 chunk 275 optimal weight: 20.0000 chunk 276 optimal weight: 0.7980 chunk 251 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 335 optimal weight: 50.0000 chunk 117 optimal weight: 0.9980 chunk 357 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 356 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN 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 G 105 GLN 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 99 GLN R 37 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 = 0.4509 r_free = 0.4509 target = 0.228216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.175726 restraints weight = 33200.931| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 3.42 r_work: 0.3420 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32148 Z= 0.130 Angle : 0.682 9.730 44007 Z= 0.326 Chirality : 0.046 0.306 5334 Planarity : 0.005 0.129 5301 Dihedral : 10.982 157.818 7474 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.73 % Favored : 93.95 % Rotamer: Outliers : 6.88 % Allowed : 33.12 % Favored : 60.01 % 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: -1.64 (0.13), residues: 3684 helix: -1.11 (0.25), residues: 435 sheet: -0.61 (0.14), residues: 1287 loop : -1.37 (0.13), residues: 1962 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 0.011 0.001 PHE I 383 TYR 0.018 0.001 TYR D 140 ARG 0.010 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 63) link_NAG-ASN : angle 2.49396 ( 189) link_ALPHA1-6 : bond 0.00404 ( 15) link_ALPHA1-6 : angle 1.69261 ( 45) link_BETA1-4 : bond 0.00395 ( 51) link_BETA1-4 : angle 1.90585 ( 153) link_ALPHA1-2 : bond 0.00505 ( 15) link_ALPHA1-2 : angle 1.70989 ( 45) link_ALPHA1-3 : bond 0.00739 ( 15) link_ALPHA1-3 : angle 1.45631 ( 45) hydrogen bonds : bond 0.03518 ( 844) hydrogen bonds : angle 5.34876 ( 2367) SS BOND : bond 0.00551 ( 51) SS BOND : angle 1.79168 ( 102) covalent geometry : bond 0.00303 (31938) covalent geometry : angle 0.64508 (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 527 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 304 time to evaluate : 3.295 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 84 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8517 (mp) REVERT: A 130 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7875 (mp10) REVERT: A 168 LYS cc_start: 0.7409 (mmmm) cc_final: 0.6987 (pptt) REVERT: A 346 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8114 (t) REVERT: B 640 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8388 (mm-40) REVERT: B 658 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7514 (tp40) REVERT: C 94 THR cc_start: 0.7820 (OUTLIER) cc_final: 0.7287 (t) REVERT: C 193 THR cc_start: 0.4853 (OUTLIER) cc_final: 0.4632 (p) REVERT: D 11 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7323 (tp) REVERT: D 20 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7918 (mmm160) REVERT: D 79 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: D 106 VAL cc_start: 0.6207 (OUTLIER) cc_final: 0.5822 (t) REVERT: D 143 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5215 (pp20) REVERT: D 166 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7652 (tp40) REVERT: F 535 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7754 (mpt) REVERT: F 658 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: G 80 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8516 (tp) REVERT: G 94 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7206 (t) REVERT: G 100 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8078 (mtm) REVERT: G 117 LYS cc_start: 0.8048 (tttm) cc_final: 0.7672 (tmtt) REVERT: H 79 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.5973 (mp10) REVERT: I 75 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8444 (m) REVERT: I 84 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8425 (mp) REVERT: I 168 LYS cc_start: 0.7162 (mmmm) cc_final: 0.6569 (pptt) REVERT: I 205 CYS cc_start: 0.6690 (OUTLIER) cc_final: 0.6402 (m) REVERT: J 575 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: J 616 ASN cc_start: 0.8178 (p0) cc_final: 0.7852 (p0) REVERT: J 640 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8340 (mp10) REVERT: K 38 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7184 (ttm-80) REVERT: L 20 ARG cc_start: 0.7992 (mmm160) cc_final: 0.7743 (mmm160) REVERT: L 79 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.6384 (mp10) REVERT: L 143 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5450 (pp20) REVERT: M 100 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.5848 (mmm) REVERT: N 11 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6761 (mm) REVERT: N 50 ASN cc_start: 0.8159 (t0) cc_final: 0.7539 (t0) REVERT: N 85 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6671 (m-30) REVERT: O 97 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8109 (ttp-170) REVERT: O 100 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7612 (mt-10) REVERT: P 28 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6599 (mp) REVERT: P 37 GLN cc_start: 0.7098 (tt0) cc_final: 0.6771 (tp-100) REVERT: P 50 ASN cc_start: 0.8214 (t0) cc_final: 0.7512 (t0) REVERT: R 52 GLN cc_start: 0.7667 (pt0) cc_final: 0.7448 (mt0) REVERT: R 85 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6394 (m-30) outliers start: 223 outliers final: 151 residues processed: 494 average time/residue: 1.1802 time to fit residues: 719.3090 Evaluate side-chains 484 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 302 time to evaluate : 3.483 ------------------------------------------------------------------------------- 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 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 393 SER Chi-restraints excluded: chain A residue 415 THR 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 658 GLN Chi-restraints excluded: chain C residue 37 VAL 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 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 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 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 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 624 ASP 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 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 184 VAL 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 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 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 371 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 415 THR 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 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 184 VAL Chi-restraints excluded: chain L residue 7 SER 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 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 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 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU 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 78 VAL 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: 0.5980 chunk 204 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 240 optimal weight: 0.0870 chunk 293 optimal weight: 10.0000 chunk 120 optimal weight: 0.6980 chunk 185 optimal weight: 0.6980 chunk 273 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN 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 G 105 GLN H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 P 51 ASN Q 99 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.228860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.173893 restraints weight = 33281.221| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 3.64 r_work: 0.3450 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32148 Z= 0.118 Angle : 0.666 10.263 44007 Z= 0.319 Chirality : 0.046 0.308 5334 Planarity : 0.005 0.129 5301 Dihedral : 10.687 158.126 7468 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.18 % Favored : 94.49 % Rotamer: Outliers : 6.17 % Allowed : 33.77 % Favored : 60.07 % 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: -1.53 (0.13), residues: 3684 helix: -0.96 (0.25), residues: 435 sheet: -0.58 (0.14), residues: 1308 loop : -1.30 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 610 HIS 0.003 0.001 HIS I 105 PHE 0.011 0.001 PHE L 139 TYR 0.035 0.001 TYR N 87 ARG 0.009 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 63) link_NAG-ASN : angle 2.39499 ( 189) link_ALPHA1-6 : bond 0.00416 ( 15) link_ALPHA1-6 : angle 1.66827 ( 45) link_BETA1-4 : bond 0.00397 ( 51) link_BETA1-4 : angle 1.84291 ( 153) link_ALPHA1-2 : bond 0.00531 ( 15) link_ALPHA1-2 : angle 1.67706 ( 45) link_ALPHA1-3 : bond 0.00765 ( 15) link_ALPHA1-3 : angle 1.45428 ( 45) hydrogen bonds : bond 0.03366 ( 844) hydrogen bonds : angle 5.22841 ( 2367) SS BOND : bond 0.00544 ( 51) SS BOND : angle 1.72393 ( 102) covalent geometry : bond 0.00273 (31938) covalent geometry : angle 0.63062 (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 514 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 314 time to evaluate : 4.359 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: 0.8446 (mm-40) cc_final: 0.7802 (mp10) REVERT: A 168 LYS cc_start: 0.7385 (mmmm) cc_final: 0.6957 (pptt) REVERT: A 346 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8083 (t) REVERT: B 635 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7413 (mm) REVERT: B 640 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8407 (mm-40) REVERT: B 658 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7403 (tp40) REVERT: C 94 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7221 (t) REVERT: C 105 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: D 11 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7327 (tp) REVERT: D 20 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7911 (mmm160) REVERT: D 79 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: D 143 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5182 (pp20) REVERT: D 166 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7651 (tp40) REVERT: F 535 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7743 (mpt) REVERT: F 570 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7771 (m) REVERT: F 658 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: G 80 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8505 (tp) REVERT: G 94 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7099 (t) REVERT: G 100 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: G 117 LYS cc_start: 0.8024 (tttm) cc_final: 0.7644 (tmtt) REVERT: H 79 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.5971 (mp10) REVERT: I 75 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8394 (m) REVERT: I 84 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8392 (mp) REVERT: I 168 LYS cc_start: 0.7118 (mmmm) cc_final: 0.6527 (pptt) REVERT: I 205 CYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6364 (m) REVERT: J 570 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.7852 (m) REVERT: J 575 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: J 616 ASN cc_start: 0.8156 (p0) cc_final: 0.7829 (p0) REVERT: J 640 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8362 (mp10) REVERT: K 38 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8180 (ttp-170) REVERT: L 20 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7741 (mmm160) REVERT: L 79 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.6402 (mp10) REVERT: L 143 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5449 (pp20) REVERT: N 11 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6746 (mm) REVERT: N 50 ASN cc_start: 0.8050 (t0) cc_final: 0.7315 (t0) REVERT: N 85 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6709 (m-30) REVERT: O 97 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.7914 (ttp-170) REVERT: O 100 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: P 28 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6532 (mp) REVERT: P 37 GLN cc_start: 0.7156 (tt0) cc_final: 0.6883 (tp-100) REVERT: P 50 ASN cc_start: 0.8152 (t0) cc_final: 0.7400 (t0) REVERT: Q 100 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: R 85 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6354 (m-30) outliers start: 200 outliers final: 141 residues processed: 483 average time/residue: 1.5891 time to fit residues: 941.1526 Evaluate side-chains 479 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 306 time to evaluate : 3.901 ------------------------------------------------------------------------------- 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 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 346 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 422 GLN Chi-restraints excluded: chain A residue 447 SER 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 658 GLN Chi-restraints excluded: chain C residue 37 VAL 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 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 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 138 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS 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 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 624 ASP 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 100 MET 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 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 162 THR Chi-restraints excluded: chain I residue 205 CYS 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 394 THR Chi-restraints excluded: chain I residue 415 THR 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 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 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 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 100 VAL Chi-restraints excluded: chain M residue 100 SER 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 28 LEU 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 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 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: 9.9990 chunk 25 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 207 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 D 3 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN E 103 GLN F 616 ASN G 6 GLN G 105 GLN H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 P 51 ASN Q 99 GLN ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.229064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.176963 restraints weight = 33087.530| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.39 r_work: 0.3432 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 32148 Z= 0.152 Angle : 0.768 59.200 44007 Z= 0.394 Chirality : 0.046 0.426 5334 Planarity : 0.005 0.128 5301 Dihedral : 10.674 158.142 7460 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.32 % Favored : 94.35 % Rotamer: Outliers : 6.32 % Allowed : 33.43 % Favored : 60.25 % 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: -1.52 (0.13), residues: 3684 helix: -0.95 (0.25), residues: 435 sheet: -0.57 (0.14), residues: 1308 loop : -1.29 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Q 34 HIS 0.002 0.001 HIS E 105 PHE 0.011 0.001 PHE L 139 TYR 0.023 0.001 TYR N 87 ARG 0.008 0.000 ARG C 100 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 63) link_NAG-ASN : angle 2.38602 ( 189) link_ALPHA1-6 : bond 0.00417 ( 15) link_ALPHA1-6 : angle 1.66892 ( 45) link_BETA1-4 : bond 0.00430 ( 51) link_BETA1-4 : angle 1.85758 ( 153) link_ALPHA1-2 : bond 0.00523 ( 15) link_ALPHA1-2 : angle 1.66737 ( 45) link_ALPHA1-3 : bond 0.00850 ( 15) link_ALPHA1-3 : angle 1.47648 ( 45) hydrogen bonds : bond 0.03412 ( 844) hydrogen bonds : angle 5.22629 ( 2367) SS BOND : bond 0.00577 ( 51) SS BOND : angle 1.70018 ( 102) covalent geometry : bond 0.00345 (31938) covalent geometry : angle 0.73880 (43428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26512.08 seconds wall clock time: 457 minutes 39.65 seconds (27459.65 seconds total)