Starting phenix.real_space_refine on Mon Aug 25 22:15:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ttw_41613/08_2025/8ttw_41613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ttw_41613/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ttw_41613/08_2025/8ttw_41613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ttw_41613/08_2025/8ttw_41613.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ttw_41613/08_2025/8ttw_41613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ttw_41613/08_2025/8ttw_41613.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.91, per 1000 atoms: 0.22 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: 3.23 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.16 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: 5.63 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4866 1.31 - 1.45: 9602 1.45 - 1.59: 17266 1.59 - 1.72: 0 1.72 - 1.86: 204 Bond restraints: 31938 Sorted by residual: bond pdb=" C12 83J A 605 " pdb=" N02 83J A 605 " ideal model delta sigma weight residual 1.339 1.454 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C12 83J I 605 " pdb=" N02 83J I 605 " ideal model delta sigma weight residual 1.339 1.454 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C12 83J E 605 " pdb=" N02 83J E 605 " ideal model delta sigma weight residual 1.339 1.453 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C13 83J E 605 " pdb=" N05 83J E 605 " ideal model delta sigma weight residual 1.353 1.458 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C13 83J I 605 " pdb=" N05 83J I 605 " ideal model delta sigma weight residual 1.353 1.458 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 31933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 43039 3.75 - 7.50: 357 7.50 - 11.25: 17 11.25 - 15.00: 3 15.00 - 18.75: 12 Bond angle restraints: 43428 Sorted by residual: angle pdb=" C13 83J A 605 " pdb=" C15 83J A 605 " pdb=" C20 83J A 605 " ideal model delta sigma weight residual 118.87 100.12 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C13 83J E 605 " pdb=" C15 83J E 605 " pdb=" C20 83J E 605 " ideal model delta sigma weight residual 118.87 100.18 18.69 3.00e+00 1.11e-01 3.88e+01 angle pdb=" C13 83J I 605 " pdb=" C15 83J I 605 " pdb=" C20 83J I 605 " ideal model delta sigma weight residual 118.87 100.20 18.67 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C25 83J A 605 " pdb=" C22 83J A 605 " pdb=" O11 83J A 605 " ideal model delta sigma weight residual 124.45 105.98 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C25 83J E 605 " pdb=" C22 83J E 605 " pdb=" O11 83J E 605 " ideal model delta sigma weight residual 124.45 106.10 18.35 3.00e+00 1.11e-01 3.74e+01 ... (remaining 43423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 19355 29.88 - 59.76: 1525 59.76 - 89.64: 171 89.64 - 119.52: 36 119.52 - 149.39: 6 Dihedral angle restraints: 21093 sinusoidal: 10317 harmonic: 10776 Sorted by residual: dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 1.69 -87.69 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 179.17 -86.17 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS P 23 " pdb=" SG CYS P 23 " pdb=" SG CYS P 88 " pdb=" CB CYS P 88 " ideal model delta sinusoidal sigma weight residual 93.00 6.97 86.03 1 1.00e+01 1.00e-02 8.94e+01 ... (remaining 21090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5074 0.104 - 0.207: 235 0.207 - 0.311: 17 0.311 - 0.415: 6 0.415 - 0.518: 2 Chirality restraints: 5334 Sorted by residual: chirality pdb=" CA CYS E 196 " pdb=" N CYS E 196 " pdb=" C CYS E 196 " pdb=" CB CYS E 196 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 88 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" C1 NAG 4 1 " pdb=" ND2 ASN I 363 " pdb=" C2 NAG 4 1 " pdb=" O5 NAG 4 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 5331 not shown) Planarity restraints: 5364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR L 140 " -0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C TYR L 140 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR L 140 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO L 141 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS I 205 " -0.020 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C CYS I 205 " 0.066 2.00e-02 2.50e+03 pdb=" O CYS I 205 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO I 206 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 205 " 0.019 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C CYS A 205 " -0.062 2.00e-02 2.50e+03 pdb=" O CYS A 205 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 206 " 0.021 2.00e-02 2.50e+03 ... (remaining 5361 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 383 2.54 - 3.13: 24507 3.13 - 3.72: 45146 3.72 - 4.31: 68814 4.31 - 4.90: 116490 Nonbonded interactions: 255340 Sorted by model distance: nonbonded pdb=" O3 NAG I 604 " pdb=" O7 NAG I 604 " model vdw 1.953 3.040 nonbonded pdb=" O3 NAG E 604 " pdb=" O7 NAG E 604 " model vdw 1.960 3.040 nonbonded pdb=" O3 NAG X 2 " pdb=" O7 NAG X 2 " model vdw 1.963 3.040 nonbonded pdb=" O3 NAG V 2 " pdb=" O7 NAG V 2 " model vdw 1.966 3.040 nonbonded pdb=" O3 NAG T 2 " pdb=" O7 NAG T 2 " model vdw 1.976 3.040 ... (remaining 255335 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'c' selection = chain 'o' } ncs_group { reference = chain '1' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = (chain '3' and (resid 1 or resid 4 through 9)) selection = (chain 'b' and (resid 2 or resid 5 through 10)) selection = (chain 'f' and (resid 1 or resid 4 through 9)) selection = (chain 'n' and (resid 2 or resid 5 through 10)) selection = (chain 'r' and (resid 1 or resid 4 through 9)) selection = (chain 'z' and (resid 2 or resid 5 through 10)) } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.74 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.170 Set scattering table: 0.080 Process input model: 27.430 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.500 ------------------------------------------------------------------------------- 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 : 31.66 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (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 ARG 0.006 0.000 ARG F 588 TYR 0.017 0.001 TYR H 91 PHE 0.009 0.001 PHE E 391 TRP 0.018 0.001 TRP I 69 HIS 0.003 0.001 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00532 (31938) covalent geometry : angle 0.85523 (43428) SS BOND : bond 0.00555 ( 51) SS BOND : angle 2.64816 ( 102) hydrogen bonds : bond 0.27746 ( 844) hydrogen bonds : angle 11.24124 ( 2367) 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) 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_NAG-ASN : bond 0.00423 ( 63) link_NAG-ASN : angle 2.55383 ( 189) *********************** 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 : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 61 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6974 (mtm110) REVERT: L 79 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.6461 (mp10) REVERT: L 107 LYS cc_start: 0.6585 (OUTLIER) cc_final: 0.6198 (mmtt) outliers start: 338 outliers final: 305 residues processed: 644 average time/residue: 0.4767 time to fit residues: 377.3280 Evaluate side-chains 634 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 313 poor density : 321 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 E 195 ASN F 630 GLN H 3 GLN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.223335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.168980 restraints weight = 33226.472| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 3.76 r_work: 0.3321 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 32148 Z= 0.226 Angle : 0.820 15.153 44007 Z= 0.395 Chirality : 0.051 0.279 5334 Planarity : 0.006 0.148 5301 Dihedral : 15.129 155.480 7848 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.14 % Favored : 92.37 % Rotamer: Outliers : 13.17 % Allowed : 25.84 % Favored : 60.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.13), residues: 3684 helix: -2.66 (0.21), residues: 435 sheet: -0.87 (0.14), residues: 1272 loop : -1.59 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 476 TYR 0.037 0.002 TYR H 140 PHE 0.015 0.002 PHE L 118 TRP 0.018 0.002 TRP J 610 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00537 (31938) covalent geometry : angle 0.78163 (43428) SS BOND : bond 0.00631 ( 51) SS BOND : angle 1.96083 ( 102) hydrogen bonds : bond 0.05757 ( 844) hydrogen bonds : angle 7.16962 ( 2367) link_ALPHA1-2 : bond 0.00455 ( 15) link_ALPHA1-2 : angle 1.92870 ( 45) link_ALPHA1-3 : bond 0.00600 ( 15) link_ALPHA1-3 : angle 1.74741 ( 45) link_ALPHA1-6 : bond 0.00342 ( 15) link_ALPHA1-6 : angle 2.03072 ( 45) link_BETA1-4 : bond 0.00440 ( 51) link_BETA1-4 : angle 2.20613 ( 153) link_NAG-ASN : bond 0.00558 ( 63) link_NAG-ASN : angle 2.74714 ( 189) *********************** 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 758 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 427 poor density : 331 time to evaluate : 0.998 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: 0.8714 (OUTLIER) cc_final: 0.8307 (mt) REVERT: A 325 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8303 (p0) REVERT: A 358 ILE cc_start: 0.8184 (pt) cc_final: 0.7967 (pp) REVERT: A 419 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7757 (ptm160) REVERT: A 456 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7638 (ttp-170) REVERT: C 30 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8435 (m-10) REVERT: D 11 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7080 (tp) REVERT: E 153 GLU cc_start: 0.6909 (tt0) cc_final: 0.6619 (tt0) REVERT: F 535 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7485 (mmt) REVERT: F 616 ASN cc_start: 0.8363 (p0) cc_final: 0.8043 (p0) REVERT: G 30 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8416 (m-10) REVERT: G 80 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8454 (tp) REVERT: H 61 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6459 (ptt-90) REVERT: H 79 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.5721 (mp10) REVERT: I 100 MET cc_start: 0.8882 (mtp) cc_final: 0.8672 (mtp) REVERT: I 140 ASP cc_start: 0.4380 (OUTLIER) cc_final: 0.4151 (t70) REVERT: I 189 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.6396 (tmtt) REVERT: I 268 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7452 (mt-10) REVERT: I 360 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8161 (ptt-90) REVERT: I 456 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7468 (ttp-170) REVERT: J 575 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8060 (tp-100) REVERT: J 640 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: J 654 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5746 (tt0) REVERT: K 13 LYS cc_start: 0.8186 (mmpt) cc_final: 0.7813 (mmtt) REVERT: L 20 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7405 (mmm160) REVERT: L 61 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6594 (ptt-90) REVERT: L 65 SER cc_start: 0.7441 (OUTLIER) cc_final: 0.7235 (m) REVERT: L 79 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.5800 (mp10) REVERT: M 77 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6381 (pm20) REVERT: M 100 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.5959 (mmm) REVERT: N 11 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6801 (mm) REVERT: O 29 MET cc_start: 0.3630 (OUTLIER) cc_final: 0.3380 (pmt) REVERT: O 77 GLN cc_start: 0.6560 (OUTLIER) cc_final: 0.6209 (pm20) REVERT: P 28 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6643 (mp) REVERT: P 50 ASN cc_start: 0.8119 (t0) cc_final: 0.7600 (t0) REVERT: Q 77 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6219 (pm20) outliers start: 427 outliers final: 249 residues processed: 692 average time/residue: 0.4897 time to fit residues: 414.7400 Evaluate side-chains 584 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 277 poor density : 307 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 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 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 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 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 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 648 GLU 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 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 97 THR 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 278 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 306 SER 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 F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain 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 54 LEU Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 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 140 ASP 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 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 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 I residue 456 ARG 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 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 100 MET 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 333 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 290 optimal weight: 40.0000 chunk 317 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 62 optimal weight: 0.0010 chunk 246 optimal weight: 5.9990 chunk 320 optimal weight: 6.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- 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** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 137 ASN I 183 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN L 166 GLN N 37 GLN N 51 ASN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.220907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.165181 restraints weight = 33186.112| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 4.04 r_work: 0.3273 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 32148 Z= 0.315 Angle : 0.877 11.331 44007 Z= 0.421 Chirality : 0.054 0.290 5334 Planarity : 0.006 0.137 5301 Dihedral : 14.190 155.053 7645 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.27 % Favored : 92.26 % Rotamer: Outliers : 12.89 % Allowed : 27.38 % Favored : 59.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.13), residues: 3684 helix: -2.48 (0.22), residues: 435 sheet: -0.98 (0.14), residues: 1290 loop : -1.68 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 476 TYR 0.033 0.002 TYR H 140 PHE 0.014 0.002 PHE G 91 TRP 0.022 0.002 TRP J 610 HIS 0.007 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00765 (31938) covalent geometry : angle 0.83434 (43428) SS BOND : bond 0.00841 ( 51) SS BOND : angle 2.55428 ( 102) hydrogen bonds : bond 0.05709 ( 844) hydrogen bonds : angle 6.66017 ( 2367) link_ALPHA1-2 : bond 0.00390 ( 15) link_ALPHA1-2 : angle 2.01075 ( 45) link_ALPHA1-3 : bond 0.00590 ( 15) link_ALPHA1-3 : angle 1.57154 ( 45) link_ALPHA1-6 : bond 0.00407 ( 15) link_ALPHA1-6 : angle 2.05901 ( 45) link_BETA1-4 : bond 0.00485 ( 51) link_BETA1-4 : angle 2.35295 ( 153) link_NAG-ASN : bond 0.00614 ( 63) link_NAG-ASN : angle 2.95063 ( 189) *********************** 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 737 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 418 poor density : 319 time to evaluate : 0.875 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: A 125 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8334 (mt) REVERT: A 358 ILE cc_start: 0.8182 (pt) cc_final: 0.7972 (pp) REVERT: A 419 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7823 (ptm160) REVERT: A 456 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7735 (ttp-170) REVERT: B 658 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: C 30 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8426 (m-10) REVERT: D 11 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7388 (tp) REVERT: E 153 GLU cc_start: 0.6972 (tt0) cc_final: 0.6517 (pt0) REVERT: F 535 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7613 (mmt) REVERT: F 658 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: G 30 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8552 (m-10) REVERT: G 105 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: G 179 SER cc_start: 0.7530 (OUTLIER) cc_final: 0.6726 (p) REVERT: H 61 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6420 (ptt-90) REVERT: H 79 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.5727 (mp10) REVERT: I 84 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8524 (mp) REVERT: I 189 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.6448 (tmtt) REVERT: I 265 LEU cc_start: 0.8351 (mt) cc_final: 0.8145 (OUTLIER) REVERT: I 360 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8217 (ptt-90) REVERT: J 568 LEU cc_start: 0.7571 (tp) cc_final: 0.7305 (tp) REVERT: J 575 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8093 (tp-100) REVERT: J 640 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8231 (mp10) REVERT: J 654 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5724 (tt0) REVERT: K 30 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8475 (m-10) REVERT: K 69 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7964 (mm) REVERT: K 175 LEU cc_start: 0.6547 (mm) cc_final: 0.5816 (mm) REVERT: L 20 ARG cc_start: 0.7664 (mtp85) cc_final: 0.7462 (mmm160) REVERT: L 61 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6545 (ptt-90) REVERT: L 79 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6127 (mp10) REVERT: N 11 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6754 (mm) REVERT: N 50 ASN cc_start: 0.8069 (t0) cc_final: 0.7559 (t0) REVERT: O 29 MET cc_start: 0.3593 (OUTLIER) cc_final: 0.3325 (pmt) REVERT: P 50 ASN cc_start: 0.8300 (t0) cc_final: 0.7690 (t0) outliers start: 418 outliers final: 262 residues processed: 662 average time/residue: 0.4939 time to fit residues: 399.1135 Evaluate side-chains 596 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 286 poor density : 310 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 248 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 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP 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 574 LYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR 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 634 GLU 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 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 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 543 ASN 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 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 30 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 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 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 47 ASP 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 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 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 J residue 663 LEU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 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 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 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 29 MET Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain 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 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 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 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 97 SER 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 11 optimal weight: 3.9990 chunk 71 optimal weight: 30.0000 chunk 224 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 331 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 358 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 577 GLN B 651 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN G 6 GLN G 105 GLN 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 ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 77 GLN N 37 GLN ** N 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4469 r_free = 0.4469 target = 0.223737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.169989 restraints weight = 32996.448| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.51 r_work: 0.3341 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 32148 Z= 0.202 Angle : 0.780 12.369 44007 Z= 0.371 Chirality : 0.050 0.299 5334 Planarity : 0.006 0.142 5301 Dihedral : 13.202 155.546 7603 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.43 % Favored : 93.16 % Rotamer: Outliers : 11.44 % Allowed : 28.71 % Favored : 59.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.13), residues: 3684 helix: -2.16 (0.23), residues: 435 sheet: -0.94 (0.14), residues: 1299 loop : -1.58 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 500 TYR 0.027 0.002 TYR H 140 PHE 0.014 0.002 PHE G 91 TRP 0.018 0.002 TRP F 610 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00485 (31938) covalent geometry : angle 0.73922 (43428) SS BOND : bond 0.00841 ( 51) SS BOND : angle 2.30146 ( 102) hydrogen bonds : bond 0.04548 ( 844) hydrogen bonds : angle 6.22406 ( 2367) link_ALPHA1-2 : bond 0.00482 ( 15) link_ALPHA1-2 : angle 1.85060 ( 45) link_ALPHA1-3 : bond 0.00677 ( 15) link_ALPHA1-3 : angle 1.55615 ( 45) link_ALPHA1-6 : bond 0.00380 ( 15) link_ALPHA1-6 : angle 1.93056 ( 45) link_BETA1-4 : bond 0.00389 ( 51) link_BETA1-4 : angle 2.13535 ( 153) link_NAG-ASN : bond 0.00500 ( 63) link_NAG-ASN : angle 2.72419 ( 189) *********************** 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 685 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 371 poor density : 314 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8289 (mt) REVERT: A 456 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7534 (ttp-110) REVERT: C 30 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8419 (m-10) REVERT: C 69 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8088 (mm) REVERT: C 100 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8708 (mmt) REVERT: C 179 SER cc_start: 0.7782 (OUTLIER) cc_final: 0.6913 (p) REVERT: D 11 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7324 (tp) REVERT: E 153 GLU cc_start: 0.6904 (tt0) cc_final: 0.6434 (pt0) REVERT: F 535 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7786 (mpt) REVERT: F 658 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7486 (tp40) REVERT: G 30 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.8439 (m-10) REVERT: G 105 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7928 (pt0) REVERT: H 20 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7262 (mtm180) REVERT: H 47 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8484 (mt) REVERT: H 61 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6648 (ptt-90) REVERT: H 79 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.5713 (mp10) REVERT: I 84 ILE cc_start: 0.8812 (OUTLIER) cc_final: 0.8464 (mp) REVERT: I 360 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8135 (ptt-90) REVERT: J 568 LEU cc_start: 0.7589 (tp) cc_final: 0.7321 (tp) REVERT: J 575 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8031 (tp-100) REVERT: J 616 ASN cc_start: 0.8311 (p0) cc_final: 0.7986 (p0) REVERT: J 640 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8228 (mp10) REVERT: J 654 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5459 (tt0) REVERT: K 66 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8114 (ttt90) REVERT: L 65 SER cc_start: 0.7483 (OUTLIER) cc_final: 0.7255 (m) REVERT: L 79 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.6137 (mp10) REVERT: L 166 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7861 (tp40) REVERT: M 100 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: N 11 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6774 (mm) REVERT: N 50 ASN cc_start: 0.8150 (t0) cc_final: 0.7557 (t0) REVERT: O 97 ARG cc_start: 0.8423 (ttp-170) cc_final: 0.8121 (ttp-170) REVERT: P 50 ASN cc_start: 0.8353 (t0) cc_final: 0.7709 (t0) REVERT: P 79 GLU cc_start: 0.5337 (OUTLIER) cc_final: 0.5067 (pp20) outliers start: 371 outliers final: 238 residues processed: 615 average time/residue: 0.4863 time to fit residues: 365.3389 Evaluate side-chains 566 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 302 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 54 CYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 371 VAL 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 608 VAL Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 100 MET 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 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 107 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 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 457 ASP Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 574 LYS Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 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 47 LEU 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 54 CYS 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 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 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 265 LEU 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 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 65 SER Chi-restraints excluded: chain L residue 69 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 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 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 69 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 ARG Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 102 VAL 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 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 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 97 SER 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 53 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 349 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 90 optimal weight: 40.0000 chunk 313 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 286 optimal weight: 7.9990 chunk 274 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 3 GLN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN F 616 ASN G 6 GLN G 105 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN P 37 GLN P 51 ASN Q 3 GLN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.220580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.163087 restraints weight = 33172.594| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.88 r_work: 0.3326 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- 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 = 0.65 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 = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 32148 Z= 0.314 Angle : 0.866 12.247 44007 Z= 0.411 Chirality : 0.054 0.299 5334 Planarity : 0.006 0.140 5301 Dihedral : 13.132 155.124 7566 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.46 % Favored : 92.10 % Rotamer: Outliers : 11.69 % Allowed : 28.25 % Favored : 60.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.13), residues: 3684 helix: -2.22 (0.23), residues: 435 sheet: -0.92 (0.14), residues: 1278 loop : -1.74 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 70 TYR 0.023 0.002 TYR R 87 PHE 0.016 0.002 PHE G 91 TRP 0.022 0.002 TRP J 610 HIS 0.006 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00766 (31938) covalent geometry : angle 0.82161 (43428) SS BOND : bond 0.00853 ( 51) SS BOND : angle 2.53743 ( 102) hydrogen bonds : bond 0.05169 ( 844) hydrogen bonds : angle 6.21990 ( 2367) link_ALPHA1-2 : bond 0.00382 ( 15) link_ALPHA1-2 : angle 2.02304 ( 45) link_ALPHA1-3 : bond 0.00587 ( 15) link_ALPHA1-3 : angle 1.58905 ( 45) link_ALPHA1-6 : bond 0.00439 ( 15) link_ALPHA1-6 : angle 2.12654 ( 45) link_BETA1-4 : bond 0.00486 ( 51) link_BETA1-4 : angle 2.38396 ( 153) link_NAG-ASN : bond 0.00606 ( 63) link_NAG-ASN : angle 2.94873 ( 189) *********************** 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 683 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 379 poor density : 304 time to evaluate : 1.134 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: 0.8811 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 125 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8265 (mt) REVERT: C 30 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8337 (m-10) REVERT: C 179 SER cc_start: 0.7584 (OUTLIER) cc_final: 0.6752 (p) REVERT: D 11 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7350 (tp) REVERT: D 79 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6247 (mp10) REVERT: E 153 GLU cc_start: 0.6795 (tt0) cc_final: 0.6320 (pt0) REVERT: F 535 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7747 (mpt) REVERT: F 658 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7401 (tp40) REVERT: G 30 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8361 (m-10) REVERT: H 20 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7255 (mtm180) REVERT: H 47 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8209 (mt) REVERT: H 61 ARG cc_start: 0.6850 (OUTLIER) cc_final: 0.6227 (ptt-90) REVERT: H 79 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.5609 (mp10) REVERT: I 84 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8439 (mp) REVERT: I 205 CYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6350 (m) REVERT: I 360 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8061 (ptt-90) REVERT: J 575 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7916 (tp-100) REVERT: J 616 ASN cc_start: 0.8279 (p0) cc_final: 0.7919 (p0) REVERT: J 640 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8096 (mp10) REVERT: J 654 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5467 (tt0) REVERT: K 66 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.8021 (ttt90) REVERT: L 79 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.5973 (mp10) REVERT: L 143 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.5356 (tm-30) REVERT: M 100 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: N 11 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6717 (mm) REVERT: N 50 ASN cc_start: 0.8162 (t0) cc_final: 0.7196 (t0) REVERT: N 79 GLU cc_start: 0.5200 (OUTLIER) cc_final: 0.4807 (pp20) REVERT: O 97 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7902 (ttp-170) REVERT: P 50 ASN cc_start: 0.8255 (t0) cc_final: 0.7590 (t0) REVERT: R 90 MET cc_start: 0.8716 (tpp) cc_final: 0.8233 (mmt) outliers start: 379 outliers final: 265 residues processed: 623 average time/residue: 0.5338 time to fit residues: 408.8813 Evaluate side-chains 584 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 290 poor density : 294 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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 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 356 ASN Chi-restraints excluded: chain A residue 358 ILE 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 422 GLN Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 606 THR 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 624 ASP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 640 GLN Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 133 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 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 161 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 167 ASP Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 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 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 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 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 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 7 SER Chi-restraints excluded: chain H residue 20 ARG Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU 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 106 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain 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 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 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 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 209 SER Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 356 ASN Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain J residue 663 LEU 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 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 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 N residue 11 LEU Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 33 VAL 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 79 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 25 ARG Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 69 THR Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 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 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 72 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER 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 340 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 chunk 196 optimal weight: 40.0000 chunk 274 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 346 optimal weight: 40.0000 chunk 89 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 283 optimal weight: 0.0970 overall best weight: 1.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN F 616 ASN G 6 GLN G 105 GLN ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 100 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 37 GLN N 51 ASN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 99 GLN P 37 GLN P 51 ASN Q 3 GLN Q 99 GLN R 37 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.224728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.170372 restraints weight = 32935.606| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.61 r_work: 0.3366 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32148 Z= 0.163 Angle : 0.738 11.389 44007 Z= 0.351 Chirality : 0.048 0.303 5334 Planarity : 0.005 0.137 5301 Dihedral : 12.214 155.739 7552 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.94 % Favored : 93.73 % Rotamer: Outliers : 10.45 % Allowed : 29.54 % Favored : 60.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.13), residues: 3684 helix: -1.87 (0.24), residues: 435 sheet: -0.88 (0.14), residues: 1299 loop : -1.57 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 500 TYR 0.022 0.001 TYR H 140 PHE 0.012 0.001 PHE I 383 TRP 0.017 0.001 TRP F 610 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00384 (31938) covalent geometry : angle 0.69678 (43428) SS BOND : bond 0.00613 ( 51) SS BOND : angle 2.17052 ( 102) hydrogen bonds : bond 0.04083 ( 844) hydrogen bonds : angle 5.88345 ( 2367) link_ALPHA1-2 : bond 0.00516 ( 15) link_ALPHA1-2 : angle 1.79884 ( 45) link_ALPHA1-3 : bond 0.00727 ( 15) link_ALPHA1-3 : angle 1.50989 ( 45) link_ALPHA1-6 : bond 0.00467 ( 15) link_ALPHA1-6 : angle 1.89819 ( 45) link_BETA1-4 : bond 0.00384 ( 51) link_BETA1-4 : angle 2.08081 ( 153) link_NAG-ASN : bond 0.00548 ( 63) link_NAG-ASN : angle 2.64264 ( 189) *********************** 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 650 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 339 poor density : 311 time to evaluate : 0.835 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: A 84 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8549 (mp) REVERT: A 168 LYS cc_start: 0.7069 (mmmm) cc_final: 0.6427 (pptt) REVERT: A 419 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7682 (ptm160) REVERT: A 428 GLN cc_start: 0.5992 (OUTLIER) cc_final: 0.5478 (mp-120) REVERT: A 456 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7642 (ttp-170) REVERT: B 658 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: C 69 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7810 (mm) REVERT: C 179 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.6918 (p) REVERT: D 11 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7344 (tp) REVERT: E 153 GLU cc_start: 0.6834 (tt0) cc_final: 0.6451 (tt0) REVERT: F 535 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7777 (mpt) REVERT: F 542 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7528 (ptt90) REVERT: F 658 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7421 (tp40) REVERT: G 30 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8464 (m-10) REVERT: G 179 SER cc_start: 0.7569 (OUTLIER) cc_final: 0.6775 (p) REVERT: H 20 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7292 (mtm180) REVERT: H 47 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8421 (mt) REVERT: H 79 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.5796 (mp10) REVERT: I 84 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8425 (mp) REVERT: I 167 ASP cc_start: 0.8202 (m-30) cc_final: 0.7866 (m-30) REVERT: I 360 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8071 (ptt-90) REVERT: J 575 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7958 (tp-100) REVERT: J 616 ASN cc_start: 0.8217 (p0) cc_final: 0.7903 (p0) REVERT: J 640 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8204 (mp10) REVERT: J 654 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5444 (tt0) REVERT: K 66 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8089 (ttt90) REVERT: L 79 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6119 (mp10) REVERT: L 143 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.5308 (tm-30) REVERT: M 100 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: N 11 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6833 (mm) REVERT: N 50 ASN cc_start: 0.8263 (t0) cc_final: 0.7257 (t0) REVERT: N 79 GLU cc_start: 0.5364 (OUTLIER) cc_final: 0.5014 (pp20) REVERT: O 94 THR cc_start: 0.7199 (OUTLIER) cc_final: 0.6993 (m) REVERT: O 97 ARG cc_start: 0.8373 (ttp-170) cc_final: 0.8120 (ttp-170) REVERT: O 100 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: P 28 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6601 (mp) REVERT: P 37 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6791 (tp-100) REVERT: P 50 ASN cc_start: 0.8339 (t0) cc_final: 0.7664 (t0) REVERT: P 79 GLU cc_start: 0.5449 (OUTLIER) cc_final: 0.5196 (pp20) REVERT: Q 29 MET cc_start: 0.3241 (pmm) cc_final: 0.2876 (pmm) REVERT: R 90 MET cc_start: 0.8607 (tpp) cc_final: 0.8275 (mmt) outliers start: 339 outliers final: 213 residues processed: 591 average time/residue: 0.5228 time to fit residues: 379.9075 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 : 1.039 ------------------------------------------------------------------------------- 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 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 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 358 ILE 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 428 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 613 SER Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 142 VAL 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 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 107 LYS 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 125 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain E residue 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 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 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 648 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 30 PHE Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 156 SER 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 20 ARG Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 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 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 205 CYS Chi-restraints excluded: chain I residue 209 SER 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 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 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 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 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 79 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 37 GLN Chi-restraints excluded: chain P residue 45 ILE 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 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 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 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER 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 94 optimal weight: 20.0000 chunk 108 optimal weight: 0.0970 chunk 100 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 362 optimal weight: 20.0000 chunk 154 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 315 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 124 GLN D 166 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 ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN M 3 GLN M 99 GLN N 37 GLN N 51 ASN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Q 99 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.223165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.171671 restraints weight = 33129.464| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 3.23 r_work: 0.3383 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 32148 Z= 0.210 Angle : 0.767 11.424 44007 Z= 0.364 Chirality : 0.050 0.303 5334 Planarity : 0.005 0.137 5301 Dihedral : 12.051 155.735 7523 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.89 % Favored : 92.78 % Rotamer: Outliers : 9.99 % Allowed : 30.00 % Favored : 60.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.13), residues: 3684 helix: -1.81 (0.24), residues: 435 sheet: -0.82 (0.14), residues: 1290 loop : -1.61 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 469 TYR 0.023 0.002 TYR L 140 PHE 0.014 0.002 PHE G 91 TRP 0.019 0.002 TRP J 610 HIS 0.004 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00509 (31938) covalent geometry : angle 0.72484 (43428) SS BOND : bond 0.00718 ( 51) SS BOND : angle 2.29132 ( 102) hydrogen bonds : bond 0.04355 ( 844) hydrogen bonds : angle 5.83361 ( 2367) link_ALPHA1-2 : bond 0.00439 ( 15) link_ALPHA1-2 : angle 1.87188 ( 45) link_ALPHA1-3 : bond 0.00654 ( 15) link_ALPHA1-3 : angle 1.48150 ( 45) link_ALPHA1-6 : bond 0.00411 ( 15) link_ALPHA1-6 : angle 1.83439 ( 45) link_BETA1-4 : bond 0.00440 ( 51) link_BETA1-4 : angle 2.18880 ( 153) link_NAG-ASN : bond 0.00531 ( 63) link_NAG-ASN : angle 2.72392 ( 189) *********************** 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 628 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 324 poor density : 304 time to evaluate : 1.043 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: A 84 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8532 (mp) REVERT: A 168 LYS cc_start: 0.7006 (mmmm) cc_final: 0.6447 (pptt) REVERT: A 419 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7686 (ptm160) REVERT: A 456 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7623 (ttp-170) REVERT: B 658 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: C 30 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8318 (m-10) REVERT: C 69 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7698 (mm) REVERT: C 179 SER cc_start: 0.7718 (OUTLIER) cc_final: 0.6888 (p) REVERT: D 11 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7318 (tp) REVERT: D 79 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6287 (mp10) REVERT: D 143 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5193 (pp20) REVERT: E 153 GLU cc_start: 0.6730 (tt0) cc_final: 0.6378 (tt0) REVERT: E 228 CYS cc_start: 0.8187 (t) cc_final: 0.7941 (t) REVERT: F 542 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7402 (ptt90) REVERT: F 658 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7362 (tp40) REVERT: G 30 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8349 (m-10) REVERT: G 80 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8392 (tp) REVERT: G 179 SER cc_start: 0.7529 (OUTLIER) cc_final: 0.6734 (p) REVERT: H 47 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8393 (mt) REVERT: H 79 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.5719 (mp10) REVERT: I 84 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8400 (mp) REVERT: I 205 CYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6404 (m) REVERT: I 308 ARG cc_start: 0.8861 (mtm-85) cc_final: 0.8652 (mtm-85) REVERT: I 360 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8012 (ptt-90) REVERT: J 568 LEU cc_start: 0.7388 (tp) cc_final: 0.7176 (tp) REVERT: J 575 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7847 (tp-100) REVERT: J 616 ASN cc_start: 0.8209 (p0) cc_final: 0.7855 (p0) REVERT: J 640 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: J 654 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5505 (tt0) REVERT: K 66 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8041 (ttt90) REVERT: L 79 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6062 (mp10) REVERT: L 143 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5564 (pp20) REVERT: M 100 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: M 100 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.5868 (mmm) REVERT: N 11 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6794 (mm) REVERT: N 50 ASN cc_start: 0.8245 (t0) cc_final: 0.7221 (t0) REVERT: N 79 GLU cc_start: 0.5434 (OUTLIER) cc_final: 0.5076 (pp20) REVERT: N 85 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6529 (m-30) REVERT: O 97 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.7936 (ttp-170) REVERT: O 100 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: P 50 ASN cc_start: 0.8332 (t0) cc_final: 0.7661 (t0) REVERT: P 79 GLU cc_start: 0.5488 (OUTLIER) cc_final: 0.5252 (pp20) REVERT: P 85 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6627 (m-30) REVERT: Q 29 MET cc_start: 0.3215 (pmm) cc_final: 0.2860 (pmm) REVERT: R 90 MET cc_start: 0.8636 (tpp) cc_final: 0.8227 (mmt) outliers start: 324 outliers final: 224 residues processed: 577 average time/residue: 0.5228 time to fit residues: 370.9467 Evaluate side-chains 551 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 258 poor density : 293 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 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 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 358 ILE 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 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 604 CYS 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 658 GLN 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 142 VAL Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 26 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 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 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 189 LYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 341 THR Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 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 648 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain F residue 663 LEU 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 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 7 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 133 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain 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 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 162 THR Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 280 ASN Chi-restraints excluded: chain I residue 303 THR Chi-restraints excluded: chain I residue 306 SER Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain I residue 360 ARG Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 575 GLN Chi-restraints excluded: chain J residue 604 CYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 608 VAL Chi-restraints excluded: chain J residue 613 SER Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 649 SER Chi-restraints excluded: chain J residue 654 GLU Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 66 ARG Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 156 SER Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 75 LYS Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 100 MET Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 33 VAL 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 79 GLU Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 97 SER Chi-restraints excluded: chain N residue 98 PHE Chi-restraints excluded: chain O residue 31 ASN Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 75 LYS Chi-restraints excluded: chain O residue 89 VAL Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 100 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 33 VAL Chi-restraints excluded: chain P residue 45 ILE 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 23 SER 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 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 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER 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 229 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 107 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 361 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 166 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 3 GLN H 100 GLN K 6 GLN K 105 GLN L 3 GLN L 124 GLN L 166 GLN M 3 GLN M 99 GLN N 51 ASN O 3 GLN O 99 GLN P 51 ASN Q 3 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.227053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.173991 restraints weight = 33226.107| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 3.47 r_work: 0.3396 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32148 Z= 0.129 Angle : 0.695 10.836 44007 Z= 0.332 Chirality : 0.047 0.306 5334 Planarity : 0.005 0.135 5301 Dihedral : 11.480 156.827 7517 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.43 % Favored : 94.25 % Rotamer: Outliers : 8.29 % Allowed : 31.70 % Favored : 60.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.13), residues: 3684 helix: -1.42 (0.24), residues: 435 sheet: -0.74 (0.14), residues: 1278 loop : -1.49 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 20 TYR 0.021 0.001 TYR L 140 PHE 0.012 0.001 PHE L 139 TRP 0.015 0.001 TRP F 610 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00301 (31938) covalent geometry : angle 0.65610 (43428) SS BOND : bond 0.00592 ( 51) SS BOND : angle 1.94836 ( 102) hydrogen bonds : bond 0.03639 ( 844) hydrogen bonds : angle 5.59726 ( 2367) link_ALPHA1-2 : bond 0.00543 ( 15) link_ALPHA1-2 : angle 1.71807 ( 45) link_ALPHA1-3 : bond 0.00741 ( 15) link_ALPHA1-3 : angle 1.46351 ( 45) link_ALPHA1-6 : bond 0.00382 ( 15) link_ALPHA1-6 : angle 1.72300 ( 45) link_BETA1-4 : bond 0.00400 ( 51) link_BETA1-4 : angle 1.96829 ( 153) link_NAG-ASN : bond 0.00503 ( 63) link_NAG-ASN : angle 2.55063 ( 189) *********************** 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 584 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 315 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7802 (mp10) REVERT: A 168 LYS cc_start: 0.7167 (mmmm) cc_final: 0.6698 (pptt) REVERT: A 456 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7521 (ttp-170) REVERT: B 658 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7490 (tp40) REVERT: D 11 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7293 (tp) REVERT: D 79 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: D 143 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5186 (pp20) REVERT: E 153 GLU cc_start: 0.6725 (tt0) cc_final: 0.6464 (tt0) REVERT: E 167 ASP cc_start: 0.8008 (m-30) cc_final: 0.7724 (m-30) REVERT: E 168 LYS cc_start: 0.7054 (mmmm) cc_final: 0.6506 (pptt) REVERT: F 542 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7458 (ptt90) REVERT: F 658 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: G 105 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: G 117 LYS cc_start: 0.7973 (tttm) cc_final: 0.7658 (ttpt) REVERT: G 179 SER cc_start: 0.7520 (OUTLIER) cc_final: 0.6753 (p) REVERT: H 47 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8287 (mt) REVERT: H 79 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.5803 (mp10) REVERT: I 75 VAL cc_start: 0.8671 (p) cc_final: 0.8463 (m) REVERT: I 84 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8391 (mp) REVERT: I 167 ASP cc_start: 0.8162 (m-30) cc_final: 0.7869 (m-30) REVERT: I 168 LYS cc_start: 0.7064 (mmmm) cc_final: 0.6491 (pptt) REVERT: I 308 ARG cc_start: 0.8881 (mtm-85) cc_final: 0.8680 (mtm-85) REVERT: J 575 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: J 616 ASN cc_start: 0.8189 (p0) cc_final: 0.7866 (p0) REVERT: J 640 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: K 6 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: K 66 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8102 (ttt90) REVERT: L 79 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6251 (mp10) REVERT: L 140 TYR cc_start: 0.7030 (t80) cc_final: 0.6653 (t80) REVERT: L 143 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5500 (pp20) REVERT: M 100 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: N 11 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6783 (mm) REVERT: N 50 ASN cc_start: 0.8284 (t0) cc_final: 0.7244 (t0) REVERT: N 79 GLU cc_start: 0.5426 (OUTLIER) cc_final: 0.5078 (pp20) REVERT: N 85 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6435 (m-30) REVERT: N 90 MET cc_start: 0.8589 (tpp) cc_final: 0.8309 (mmt) REVERT: O 97 ARG cc_start: 0.8328 (ttp-170) cc_final: 0.8069 (ttp-170) REVERT: O 100 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: P 50 ASN cc_start: 0.8319 (t0) cc_final: 0.7755 (t0) REVERT: P 79 GLU cc_start: 0.5673 (OUTLIER) cc_final: 0.5434 (pp20) REVERT: P 85 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: Q 29 MET cc_start: 0.3295 (pmm) cc_final: 0.2937 (pmm) REVERT: Q 100 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: R 90 MET cc_start: 0.8533 (tpp) cc_final: 0.8238 (mmt) outliers start: 269 outliers final: 178 residues processed: 539 average time/residue: 0.5680 time to fit residues: 374.0522 Evaluate side-chains 499 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 295 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 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 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 358 ILE 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 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 598 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 51 ILE Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 107 LYS 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 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 162 THR 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 368 ASP Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 542 ARG 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 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 205 CYS Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 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 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 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 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 181 LEU 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 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 79 GLU 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 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 GLU Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain P residue 11 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 79 GLU 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 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 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 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 284 optimal weight: 4.9990 chunk 68 optimal weight: 0.0770 chunk 292 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 275 optimal weight: 20.0000 chunk 311 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 193 optimal weight: 0.0670 chunk 323 optimal weight: 0.3980 chunk 334 optimal weight: 6.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 166 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 100 GLN I 130 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN L 3 GLN L 124 GLN L 166 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 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 = 0.4496 r_free = 0.4496 target = 0.226879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.172815 restraints weight = 33252.079| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.69 r_work: 0.3386 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32148 Z= 0.137 Angle : 0.700 10.453 44007 Z= 0.334 Chirality : 0.047 0.307 5334 Planarity : 0.005 0.133 5301 Dihedral : 11.296 157.291 7500 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.78 % Favored : 93.89 % Rotamer: Outliers : 7.71 % Allowed : 32.35 % Favored : 59.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.13), residues: 3684 helix: -1.28 (0.25), residues: 435 sheet: -0.68 (0.14), residues: 1278 loop : -1.45 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 71 TYR 0.020 0.001 TYR L 140 PHE 0.012 0.001 PHE E 383 TRP 0.017 0.001 TRP B 610 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00324 (31938) covalent geometry : angle 0.66071 (43428) SS BOND : bond 0.00591 ( 51) SS BOND : angle 1.93922 ( 102) hydrogen bonds : bond 0.03649 ( 844) hydrogen bonds : angle 5.49763 ( 2367) link_ALPHA1-2 : bond 0.00494 ( 15) link_ALPHA1-2 : angle 1.73719 ( 45) link_ALPHA1-3 : bond 0.00714 ( 15) link_ALPHA1-3 : angle 1.45705 ( 45) link_ALPHA1-6 : bond 0.00381 ( 15) link_ALPHA1-6 : angle 1.70999 ( 45) link_BETA1-4 : bond 0.00402 ( 51) link_BETA1-4 : angle 1.98272 ( 153) link_NAG-ASN : bond 0.00449 ( 63) link_NAG-ASN : angle 2.57842 ( 189) *********************** 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 548 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 298 time to evaluate : 1.144 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: 0.8827 (OUTLIER) cc_final: 0.8548 (mp) REVERT: A 130 GLN cc_start: 0.8440 (mm-40) cc_final: 0.7799 (mp10) REVERT: A 456 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7450 (ttp-170) REVERT: B 640 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8457 (mm-40) REVERT: B 658 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7467 (tp40) REVERT: D 11 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7338 (tp) REVERT: D 79 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6957 (mp10) REVERT: D 143 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5219 (pp20) REVERT: E 167 ASP cc_start: 0.8047 (m-30) cc_final: 0.7777 (m-30) REVERT: F 658 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: G 94 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7118 (t) REVERT: G 117 LYS cc_start: 0.7980 (tttm) cc_final: 0.7595 (tmtt) REVERT: G 193 THR cc_start: 0.4680 (OUTLIER) cc_final: 0.4443 (p) REVERT: H 47 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8285 (mt) REVERT: H 79 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.5902 (mp10) REVERT: I 75 VAL cc_start: 0.8642 (p) cc_final: 0.8435 (m) REVERT: I 84 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8398 (mp) REVERT: I 167 ASP cc_start: 0.8184 (m-30) cc_final: 0.7878 (m-30) REVERT: I 168 LYS cc_start: 0.7062 (mmmm) cc_final: 0.6453 (pptt) REVERT: I 205 CYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6397 (m) REVERT: J 575 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: J 616 ASN cc_start: 0.8201 (p0) cc_final: 0.7862 (p0) REVERT: J 640 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: K 38 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7228 (ttm-80) REVERT: K 193 THR cc_start: 0.4401 (OUTLIER) cc_final: 0.4192 (p) REVERT: L 20 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7723 (mmm160) REVERT: L 79 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.6216 (mp10) REVERT: L 140 TYR cc_start: 0.7107 (t80) cc_final: 0.6715 (t80) REVERT: L 143 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5312 (pp20) REVERT: M 100 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8425 (mt-10) REVERT: N 11 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6791 (mm) REVERT: N 50 ASN cc_start: 0.8211 (t0) cc_final: 0.7152 (t0) REVERT: N 79 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.5021 (pp20) REVERT: N 85 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6438 (m-30) REVERT: N 90 MET cc_start: 0.8567 (tpp) cc_final: 0.8272 (mmt) REVERT: O 97 ARG cc_start: 0.8268 (ttp-170) cc_final: 0.7997 (ttp-170) REVERT: O 100 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: P 50 ASN cc_start: 0.8248 (t0) cc_final: 0.7621 (t0) REVERT: P 79 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5451 (pp20) REVERT: P 85 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6661 (m-30) REVERT: Q 29 MET cc_start: 0.3225 (pmm) cc_final: 0.2876 (pmm) REVERT: Q 100 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: R 52 GLN cc_start: 0.7537 (pt0) cc_final: 0.7186 (mt0) REVERT: R 90 MET cc_start: 0.8514 (tpp) cc_final: 0.8203 (mmt) outliers start: 250 outliers final: 179 residues processed: 511 average time/residue: 0.5605 time to fit residues: 350.0866 Evaluate side-chains 498 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 291 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 358 ILE 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 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 598 CYS 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 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 102 SER Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain 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 162 THR 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 447 SER Chi-restraints excluded: chain F residue 520 LEU 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 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 68 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 102 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 54 CYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain I residue 132 THR Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 161 MET Chi-restraints excluded: chain I residue 162 THR Chi-restraints excluded: chain I residue 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 364 SER Chi-restraints excluded: chain I residue 365 SER Chi-restraints excluded: chain I residue 371 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 570 VAL 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 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 82 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 181 LEU 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 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 79 GLU 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 70 SER 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 33 VAL Chi-restraints excluded: chain P residue 45 ILE 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 23 SER 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 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 78 VAL Chi-restraints excluded: chain R residue 85 ASP Chi-restraints excluded: chain R residue 97 SER 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 356 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 94 optimal weight: 50.0000 chunk 208 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 279 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 3 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 166 GLN E 103 GLN F 616 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN I 130 GLN J 651 ASN K 6 GLN 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 Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.227136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174323 restraints weight = 33045.676| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 3.52 r_work: 0.3392 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32148 Z= 0.139 Angle : 0.692 11.066 44007 Z= 0.330 Chirality : 0.047 0.308 5334 Planarity : 0.005 0.132 5301 Dihedral : 11.070 157.413 7496 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.94 % Favored : 93.73 % Rotamer: Outliers : 7.00 % Allowed : 32.90 % Favored : 60.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.00 % Twisted Proline : 1.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.13), residues: 3684 helix: -1.20 (0.25), residues: 435 sheet: -0.62 (0.14), residues: 1275 loop : -1.42 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 71 TYR 0.024 0.001 TYR P 87 PHE 0.012 0.001 PHE L 139 TRP 0.018 0.001 TRP J 610 HIS 0.003 0.001 HIS I 105 Details of bonding type rmsd covalent geometry : bond 0.00328 (31938) covalent geometry : angle 0.65377 (43428) SS BOND : bond 0.00596 ( 51) SS BOND : angle 1.90624 ( 102) hydrogen bonds : bond 0.03627 ( 844) hydrogen bonds : angle 5.38417 ( 2367) link_ALPHA1-2 : bond 0.00489 ( 15) link_ALPHA1-2 : angle 1.73436 ( 45) link_ALPHA1-3 : bond 0.00706 ( 15) link_ALPHA1-3 : angle 1.44790 ( 45) link_ALPHA1-6 : bond 0.00368 ( 15) link_ALPHA1-6 : angle 1.70620 ( 45) link_BETA1-4 : bond 0.00409 ( 51) link_BETA1-4 : angle 1.95806 ( 153) link_NAG-ASN : bond 0.00450 ( 63) link_NAG-ASN : angle 2.51065 ( 189) ********************** 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 525 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 298 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8570 (mp) REVERT: A 130 GLN cc_start: 0.8486 (mm-40) cc_final: 0.7849 (mp10) REVERT: A 168 LYS cc_start: 0.7392 (mmmm) cc_final: 0.6932 (pptt) REVERT: A 456 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7436 (ttp-170) REVERT: B 640 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8461 (mm-40) REVERT: B 658 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7510 (tp40) REVERT: C 105 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7789 (pm20) REVERT: D 11 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7334 (tp) REVERT: D 79 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7094 (mp10) REVERT: D 143 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5098 (pp20) REVERT: E 167 ASP cc_start: 0.8031 (m-30) cc_final: 0.7770 (m-30) REVERT: E 228 CYS cc_start: 0.8318 (t) cc_final: 0.8084 (t) REVERT: F 658 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: G 80 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8481 (tp) REVERT: G 117 LYS cc_start: 0.8036 (tttm) cc_final: 0.7665 (tmtt) REVERT: G 179 SER cc_start: 0.7463 (OUTLIER) cc_final: 0.6757 (p) REVERT: H 47 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8300 (mt) REVERT: H 79 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.5957 (mp10) REVERT: H 166 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7725 (tp40) REVERT: I 84 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8421 (mp) REVERT: I 167 ASP cc_start: 0.8203 (m-30) cc_final: 0.7901 (m-30) REVERT: I 168 LYS cc_start: 0.7114 (mmmm) cc_final: 0.6562 (pptt) REVERT: I 205 CYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6476 (m) REVERT: J 575 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: J 616 ASN cc_start: 0.8176 (p0) cc_final: 0.7842 (p0) REVERT: J 640 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8267 (mp10) REVERT: K 6 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: K 38 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7179 (ttm-80) REVERT: L 20 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7798 (mmm160) REVERT: L 79 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6474 (mp10) REVERT: L 143 GLU cc_start: 0.6245 (OUTLIER) cc_final: 0.5325 (pp20) REVERT: M 100 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: N 11 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6790 (mm) REVERT: N 50 ASN cc_start: 0.8230 (t0) cc_final: 0.7233 (t0) REVERT: N 79 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.5129 (pp20) REVERT: N 85 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: N 90 MET cc_start: 0.8439 (tpp) cc_final: 0.8217 (mmt) REVERT: O 97 ARG cc_start: 0.8295 (ttp-170) cc_final: 0.8030 (ttp-170) REVERT: O 100 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: P 50 ASN cc_start: 0.8250 (t0) cc_final: 0.7543 (t0) REVERT: P 79 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5589 (pp20) REVERT: Q 100 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: R 52 GLN cc_start: 0.7599 (pt0) cc_final: 0.7304 (mt0) REVERT: R 90 MET cc_start: 0.8501 (tpp) cc_final: 0.8239 (mmt) outliers start: 227 outliers final: 166 residues processed: 492 average time/residue: 0.5836 time to fit residues: 349.0878 Evaluate side-chains 487 residues out of total 3243 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 292 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 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 128 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 415 THR 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 598 CYS 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 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 105 GLN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 156 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 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 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 162 THR 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 447 SER Chi-restraints excluded: chain F residue 520 LEU 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 624 ASP Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 648 GLU Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain G residue 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 179 SER Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 166 GLN 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 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 364 SER Chi-restraints excluded: chain I residue 365 SER 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 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 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 67 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 116 THR Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 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 78 LEU 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 181 LEU 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 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 79 GLU 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 70 SER 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 33 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 79 GLU 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 85 ASP Chi-restraints excluded: chain R residue 97 SER 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 30 optimal weight: 0.6980 chunk 334 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 146 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 357 optimal weight: 8.9990 chunk 208 optimal weight: 0.0070 chunk 17 optimal weight: 0.0770 chunk 83 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN C 6 GLN C 105 GLN D 3 GLN ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN D 166 GLN E 103 GLN F 616 ASN G 6 GLN H 100 GLN J 651 ASN ** 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 N 52 GLN O 3 GLN O 99 GLN P 51 ASN Q 99 GLN R 37 GLN R 51 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.228714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.177159 restraints weight = 33300.206| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 3.48 r_work: 0.3411 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32148 Z= 0.118 Angle : 0.673 11.424 44007 Z= 0.323 Chirality : 0.046 0.310 5334 Planarity : 0.005 0.130 5301 Dihedral : 10.799 157.880 7480 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.62 % Favored : 94.06 % Rotamer: Outliers : 6.26 % Allowed : 33.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.13), residues: 3684 helix: -1.03 (0.25), residues: 435 sheet: -0.59 (0.14), residues: 1287 loop : -1.34 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 71 TYR 0.020 0.001 TYR P 87 PHE 0.012 0.001 PHE A 383 TRP 0.015 0.001 TRP J 610 HIS 0.003 0.001 HIS R 38 Details of bonding type rmsd covalent geometry : bond 0.00271 (31938) covalent geometry : angle 0.63740 (43428) SS BOND : bond 0.00507 ( 51) SS BOND : angle 1.74336 ( 102) hydrogen bonds : bond 0.03363 ( 844) hydrogen bonds : angle 5.24984 ( 2367) link_ALPHA1-2 : bond 0.00582 ( 15) link_ALPHA1-2 : angle 1.67328 ( 45) link_ALPHA1-3 : bond 0.00745 ( 15) link_ALPHA1-3 : angle 1.46038 ( 45) link_ALPHA1-6 : bond 0.00403 ( 15) link_ALPHA1-6 : angle 1.67395 ( 45) link_BETA1-4 : bond 0.00400 ( 51) link_BETA1-4 : angle 1.87836 ( 153) link_NAG-ASN : bond 0.00444 ( 63) link_NAG-ASN : angle 2.42481 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11749.89 seconds wall clock time: 201 minutes 2.34 seconds (12062.34 seconds total)