Starting phenix.real_space_refine on Mon Aug 25 10:15:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bio_44595/08_2025/9bio_44595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bio_44595/08_2025/9bio_44595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bio_44595/08_2025/9bio_44595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bio_44595/08_2025/9bio_44595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bio_44595/08_2025/9bio_44595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bio_44595/08_2025/9bio_44595.map" } resolution = 2.83 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= 0.011 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 141 5.16 5 C 17242 2.51 5 N 4433 2.21 5 O 5681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 27498 Number of models: 1 Model: "" Number of chains: 68 Chain: "B" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1088 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "G" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3722 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain: "S" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "U" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 97} Chain: "H" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "A" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1088 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "C" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3722 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "F" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 97} Chain: "I" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "J" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1088 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 1, 'TRANS': 134} Chain breaks: 1 Chain: "K" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3722 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain: "M" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "N" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "O" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 97} Chain: "P" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "Q" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" 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: "V" 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: "W" 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: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: "k" 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: "l" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 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: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: "y" 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: "z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "0" 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: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "U" 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: "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: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 117 Unusual residues: {'NAG': 8, 'PO4': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" 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: "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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "N" 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 Time building chain proxies: 7.47, per 1000 atoms: 0.27 Number of scatterers: 27498 At special positions: 0 Unit cell: (158.935, 153.454, 137.013, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 141 16.00 P 1 15.00 O 5681 8.00 N 4433 7.00 C 17242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 605 " - pdb=" SG CYS K 501 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.04 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.04 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.04 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 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 23 " - pdb=" SG CYS O 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " 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 W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " " MAN k 4 " - " MAN k 5 " " MAN k 5 " - " MAN k 6 " " MAN y 4 " - " MAN y 5 " " MAN y 5 " - " MAN y 6 " ALPHA1-3 " BMA 3 3 " - " MAN 3 7 " " MAN 3 4 " - " MAN 3 5 " " BMA Q 3 " - " MAN Q 6 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " MAN W 7 " - " MAN W 8 " " BMA X 3 " - " MAN X 7 " " MAN X 4 " - " MAN X 5 " " BMA b 3 " - " MAN b 7 " " MAN b 4 " - " MAN b 5 " " BMA g 3 " - " MAN g 6 " " BMA j 3 " - " MAN j 4 " " BMA k 3 " - " MAN k 4 " " MAN k 7 " - " MAN k 8 " " BMA l 3 " - " MAN l 7 " " MAN l 4 " - " MAN l 5 " " BMA p 3 " - " MAN p 7 " " MAN p 4 " - " MAN p 5 " " BMA u 3 " - " MAN u 6 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " " MAN y 7 " - " MAN y 8 " " BMA z 3 " - " MAN z 7 " " MAN z 4 " - " MAN z 5 " ALPHA1-6 " BMA 3 3 " - " MAN 3 4 " " MAN 3 4 " - " MAN 3 6 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 5 " " BMA V 3 " - " MAN V 5 " " BMA W 3 " - " MAN W 7 " " MAN W 7 " - " MAN W 9 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 6 " " BMA b 3 " - " MAN b 4 " " MAN b 4 " - " MAN b 6 " " BMA g 3 " - " MAN g 4 " " MAN g 4 " - " MAN g 5 " " BMA j 3 " - " MAN j 5 " " BMA k 3 " - " MAN k 7 " " MAN k 7 " - " MAN k 9 " " BMA l 3 " - " MAN l 4 " " MAN l 4 " - " MAN l 6 " " BMA p 3 " - " MAN p 4 " " MAN p 4 " - " MAN p 6 " " BMA u 3 " - " MAN u 4 " " MAN u 4 " - " MAN u 5 " " BMA x 3 " - " MAN x 5 " " BMA y 3 " - " MAN y 7 " " MAN y 7 " - " MAN y 9 " " BMA z 3 " - " MAN z 4 " " MAN z 4 " - " MAN z 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " 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 Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " 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 d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " BETA1-6 " NAG Q 1 " - " FUC Q 7 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG g 1 " - " FUC g 7 " " NAG u 1 " - " FUC u 7 " NAG-ASN " NAG 0 1 " - " ASN K 295 " " NAG 1 1 " - " ASN K 386 " " NAG 2 1 " - " ASN K 448 " " NAG 3 1 " - " ASN K 88 " " NAG 4 1 " - " ASN K 334 " " NAG 5 1 " - " ASN K 241 " " NAG 6 1 " - " ASN K 289 " " NAG A 701 " - " ASN A 616 " " NAG A 702 " - " ASN A 611 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 616 " " NAG B 703 " - " ASN B 611 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 234 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 392 " " NAG C 606 " - " ASN C 149 " " NAG C 607 " - " ASN C 356 " " NAG C 608 " - " ASN C 405 " " NAG C 609 " - " ASN C 339 " " NAG E 301 " - " ASN E 72 " " NAG G 601 " - " ASN G 133 " " NAG G 602 " - " ASN G 234 " " NAG G 603 " - " ASN G 301 " " NAG G 604 " - " ASN G 392 " " NAG G 605 " - " ASN G 149 " " NAG G 606 " - " ASN G 356 " " NAG G 607 " - " ASN G 405 " " NAG G 608 " - " ASN G 339 " " NAG J 701 " - " ASN J 616 " " NAG J 702 " - " ASN J 611 " " NAG K 601 " - " ASN K 133 " " NAG K 602 " - " ASN K 234 " " NAG K 603 " - " ASN K 301 " " NAG K 604 " - " ASN K 392 " " NAG K 605 " - " ASN K 149 " " NAG K 606 " - " ASN K 356 " " NAG K 607 " - " ASN K 405 " " NAG K 608 " - " ASN K 339 " " NAG N 301 " - " ASN N 72 " " NAG Q 1 " - " ASN B 625 " " NAG R 1 " - " ASN G 156 " " NAG T 1 " - " ASN G 160 " " NAG U 301 " - " ASN U 72 " " NAG V 1 " - " ASN G 197 " " NAG W 1 " - " ASN G 262 " " NAG X 1 " - " ASN G 276 " " NAG Y 1 " - " ASN G 295 " " NAG Z 1 " - " ASN G 386 " " NAG a 1 " - " ASN G 448 " " NAG b 1 " - " ASN G 88 " " NAG c 1 " - " ASN G 334 " " NAG d 1 " - " ASN G 241 " " NAG e 1 " - " ASN G 289 " " NAG f 1 " - " ASN A 637 " " NAG g 1 " - " ASN A 625 " " NAG h 1 " - " ASN C 156 " " NAG i 1 " - " ASN C 160 " " NAG j 1 " - " ASN C 197 " " NAG k 1 " - " ASN C 262 " " NAG l 1 " - " ASN C 276 " " NAG m 1 " - " ASN C 295 " " NAG n 1 " - " ASN C 386 " " NAG o 1 " - " ASN C 448 " " NAG p 1 " - " ASN C 88 " " NAG q 1 " - " ASN C 334 " " NAG r 1 " - " ASN C 241 " " NAG s 1 " - " ASN C 289 " " NAG t 1 " - " ASN J 637 " " NAG u 1 " - " ASN J 625 " " NAG v 1 " - " ASN K 156 " " NAG w 1 " - " ASN K 160 " " NAG x 1 " - " ASN K 197 " " NAG y 1 " - " ASN K 262 " " NAG z 1 " - " ASN K 276 " Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 48 sheets defined 16.6% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.938A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 551 removed outlier: 3.661A pdb=" N GLN B 550 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 removed outlier: 3.707A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.552A pdb=" N ASN B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.503A pdb=" N ASP B 659 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.966A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 126 Processing helix chain 'G' and resid 195 through 198 Processing helix chain 'G' and resid 335 through 353 removed outlier: 3.507A pdb=" N VAL G 346 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU G 351 " --> pdb=" O GLY G 347 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS G 352 " --> pdb=" O LYS G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 459B through 463 Processing helix chain 'G' and resid 476 through 481 removed outlier: 3.640A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.517A pdb=" N TYR S 32 " --> pdb=" O ILE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.832A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.235A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.974A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 removed outlier: 3.559A pdb=" N GLN A 550 " --> pdb=" O GLY A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 596 removed outlier: 3.630A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.514A pdb=" N ASN A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.543A pdb=" N ASP A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.008A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.570A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 459B through 463 Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.507A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.522A pdb=" N ASP D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.786A pdb=" N PHE I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.163A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 542 removed outlier: 4.027A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 547 through 551 removed outlier: 3.675A pdb=" N GLN J 550 " --> pdb=" O GLY J 547 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 removed outlier: 3.527A pdb=" N LYS J 574 " --> pdb=" O VAL J 570 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR J 586 " --> pdb=" O ALA J 582 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE J 592 " --> pdb=" O GLU J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 619 through 624 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 659 removed outlier: 3.503A pdb=" N ASP J 659 " --> pdb=" O ILE J 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 117 removed outlier: 4.104A pdb=" N GLU K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 126 Processing helix chain 'K' and resid 179 through 181 No H-bonds generated for 'chain 'K' and resid 179 through 181' Processing helix chain 'K' and resid 193 through 198 removed outlier: 3.978A pdb=" N ASN K 197 " --> pdb=" O ILE K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 353 removed outlier: 3.761A pdb=" N GLU K 351 " --> pdb=" O GLY K 347 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS K 352 " --> pdb=" O LYS K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 459B through 463 Processing helix chain 'K' and resid 476 through 484 removed outlier: 3.562A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLU K 482 " --> pdb=" O ASN K 478 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.894A pdb=" N ASP M 31 " --> pdb=" O ASN M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'P' and resid 83 through 87 removed outlier: 4.169A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.937A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.592A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'G' and resid 120 through 121 removed outlier: 3.958A pdb=" N VAL G 120 " --> pdb=" O GLN G 203 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 130 through 133 Processing sheet with id=AA7, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 312 removed outlier: 6.204A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 322 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 10 through 11 current: chain 'S' and resid 45 through 52 removed outlier: 3.668A pdb=" N GLN S 56 " --> pdb=" O ASN S 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 56 through 58 current: chain 'S' and resid 100B through 103 Processing sheet with id=AB2, first strand: chain 'U' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'U' and resid 53 through 54 removed outlier: 5.723A pdb=" N LEU U 46 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN U 37 " --> pdb=" O LEU U 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.614A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.760A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.524A pdb=" N GLU H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR H 68 " --> pdb=" O GLU H 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.247A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 603 through 609 removed outlier: 7.887A pdb=" N CYS A 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR C 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR A 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL C 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL A 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.524A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.991A pdb=" N VAL C 120 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.243A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 322 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AC7, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.554A pdb=" N LEU D 82 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 11 current: chain 'D' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 58 current: chain 'D' and resid 100B through 103 Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AD1, first strand: chain 'E' and resid 53 through 54 removed outlier: 5.842A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.599A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.787A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.617A pdb=" N TRP F 35 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.557A pdb=" N GLU I 81 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR I 68 " --> pdb=" O GLU I 81 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.178A pdb=" N GLU I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA I 88 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 603 through 609 removed outlier: 7.934A pdb=" N CYS J 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N TYR K 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR J 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL K 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL J 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AD9, first strand: chain 'K' and resid 75 through 76 removed outlier: 3.709A pdb=" N VAL K 75 " --> pdb=" O CYS K 54 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AE2, first strand: chain 'K' and resid 120 through 121 removed outlier: 3.902A pdb=" N VAL K 120 " --> pdb=" O GLN K 203 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 130 through 133 Processing sheet with id=AE4, first strand: chain 'K' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 259 through 261 current: chain 'K' and resid 284 through 312 removed outlier: 6.192A pdb=" N ASN K 301 " --> pdb=" O ILE K 322 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE K 322 " --> pdb=" O ASN K 301 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR K 303 " --> pdb=" O GLY K 321 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN K 315 " --> pdb=" O ILE K 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 315 through 322 current: chain 'K' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 381 through 385 current: chain 'K' and resid 465 through 470 Processing sheet with id=AE5, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 11 current: chain 'M' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 58 current: chain 'M' and resid 100B through 103 Processing sheet with id=AE7, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AE8, first strand: chain 'N' and resid 53 through 54 removed outlier: 5.892A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 4 through 7 removed outlier: 3.561A pdb=" N VAL O 19 " --> pdb=" O ILE O 75 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG O 70 " --> pdb=" O SER O 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.832A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP O 35 " --> pdb=" O VAL O 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.584A pdb=" N SER P 25 " --> pdb=" O TYR P 3 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU P 81 " --> pdb=" O THR P 68 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR P 68 " --> pdb=" O GLU P 81 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 10 through 11 removed outlier: 7.160A pdb=" N GLU P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA P 88 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY P 49 " --> pdb=" O TRP P 36 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 1827 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: 6.04 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8224 1.34 - 1.46: 7627 1.46 - 1.59: 12066 1.59 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 28103 Sorted by residual: bond pdb=" C ARG G 166 " pdb=" N ASP G 167 " ideal model delta sigma weight residual 1.335 1.302 0.033 1.39e-02 5.18e+03 5.73e+00 bond pdb=" O3 PO4 C 601 " pdb=" P PO4 C 601 " ideal model delta sigma weight residual 1.569 1.522 0.047 2.00e-02 2.50e+03 5.58e+00 bond pdb=" O2 PO4 C 601 " pdb=" P PO4 C 601 " ideal model delta sigma weight residual 1.567 1.523 0.044 2.00e-02 2.50e+03 4.94e+00 bond pdb=" O4 PO4 C 601 " pdb=" P PO4 C 601 " ideal model delta sigma weight residual 1.568 1.524 0.044 2.00e-02 2.50e+03 4.89e+00 bond pdb=" C ARG G 166 " pdb=" O ARG G 166 " ideal model delta sigma weight residual 1.236 1.209 0.028 1.26e-02 6.30e+03 4.81e+00 ... (remaining 28098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 36227 1.42 - 2.84: 1491 2.84 - 4.26: 287 4.26 - 5.68: 144 5.68 - 7.10: 82 Bond angle restraints: 38231 Sorted by residual: angle pdb=" CA CYS K 247 " pdb=" CB CYS K 247 " pdb=" SG CYS K 247 " ideal model delta sigma weight residual 114.40 121.50 -7.10 2.30e+00 1.89e-01 9.53e+00 angle pdb=" N ALA F 51 " pdb=" CA ALA F 51 " pdb=" CB ALA F 51 " ideal model delta sigma weight residual 114.17 110.74 3.43 1.14e+00 7.69e-01 9.07e+00 angle pdb=" N ARG G 166 " pdb=" CA ARG G 166 " pdb=" CB ARG G 166 " ideal model delta sigma weight residual 110.28 114.76 -4.48 1.55e+00 4.16e-01 8.36e+00 angle pdb=" C SER I 2 " pdb=" N TYR I 3 " pdb=" CA TYR I 3 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.92e+00 angle pdb=" N ILE O 29 " pdb=" CA ILE O 29 " pdb=" C ILE O 29 " ideal model delta sigma weight residual 111.90 109.79 2.11 8.10e-01 1.52e+00 6.76e+00 ... (remaining 38226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 18023 24.23 - 48.47: 731 48.47 - 72.70: 207 72.70 - 96.93: 133 96.93 - 121.16: 64 Dihedral angle restraints: 19158 sinusoidal: 10038 harmonic: 9120 Sorted by residual: dihedral pdb=" CD ARG G 166 " pdb=" NE ARG G 166 " pdb=" CZ ARG G 166 " pdb=" NH1 ARG G 166 " ideal model delta sinusoidal sigma weight residual 0.00 -85.93 85.93 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS K 218 " pdb=" SG CYS K 218 " pdb=" SG CYS K 247 " pdb=" CB CYS K 247 " ideal model delta sinusoidal sigma weight residual 93.00 32.76 60.24 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -142.38 56.38 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 19155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3978 0.058 - 0.116: 640 0.116 - 0.174: 164 0.174 - 0.232: 4 0.232 - 0.290: 18 Chirality restraints: 4804 Sorted by residual: chirality pdb=" C5 BMA b 3 " pdb=" C4 BMA b 3 " pdb=" C6 BMA b 3 " pdb=" O5 BMA b 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C5 BMA 3 3 " pdb=" C4 BMA 3 3 " pdb=" C6 BMA 3 3 " pdb=" O5 BMA 3 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C5 BMA p 3 " pdb=" C4 BMA p 3 " pdb=" C6 BMA p 3 " pdb=" O5 BMA p 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 4801 not shown) Planarity restraints: 4673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 166 " 1.106 9.50e-02 1.11e+02 4.96e-01 1.48e+02 pdb=" NE ARG G 166 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 166 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG G 166 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG G 166 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 252 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO K 253 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 99 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO F 100 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 100 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 100 " 0.020 5.00e-02 4.00e+02 ... (remaining 4670 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 194 2.52 - 3.11: 21121 3.11 - 3.71: 38176 3.71 - 4.30: 59276 4.30 - 4.90: 99590 Nonbonded interactions: 218357 Sorted by model distance: nonbonded pdb=" OG1 THR B 606 " pdb=" O VAL G 36 " model vdw 1.922 3.040 nonbonded pdb=" OG1 THR A 606 " pdb=" O VAL C 36 " model vdw 1.974 3.040 nonbonded pdb=" OG1 THR U 22 " pdb=" OE2 GLU U 70 " model vdw 2.047 3.040 nonbonded pdb=" OE2 GLU S 23 " pdb=" OG1 THR S 75 " model vdw 2.081 3.040 nonbonded pdb=" O GLN P 1 " pdb=" OG SER P 2 " model vdw 2.133 3.040 ... (remaining 218352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain 'R' selection = chain 'T' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'w' } ncs_group { reference = chain '1' selection = chain 'Z' selection = chain 'n' } ncs_group { reference = (chain '3' and resid 1 through 6) selection = (chain 'Q' and resid 1 through 6) selection = (chain 'X' and resid 1 through 6) selection = (chain 'b' and resid 1 through 6) selection = (chain 'g' and resid 1 through 6) selection = (chain 'l' and resid 1 through 6) selection = (chain 'p' and resid 1 through 6) selection = (chain 'u' and resid 1 through 6) selection = (chain 'z' and resid 1 through 6) } ncs_group { reference = chain 'A' selection = (chain 'B' and resid 517 through 702) selection = chain 'J' } ncs_group { reference = (chain 'C' and (resid 31 through 506 or resid 602 through 608)) selection = (chain 'G' and (resid 31 through 506 or resid 602 through 608)) selection = (chain 'K' and (resid 31 through 506 or resid 602 through 608)) } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'U' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'P' } ncs_group { reference = chain 'V' selection = chain 'j' selection = chain 'x' } ncs_group { reference = chain 'W' selection = chain 'k' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 29.760 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 0.047 28345 Z= 0.254 Angle : 0.785 9.235 38909 Z= 0.338 Chirality : 0.050 0.290 4804 Planarity : 0.008 0.496 4598 Dihedral : 16.748 121.165 13158 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.91 % Favored : 94.02 % Rotamer: Outliers : 0.22 % Allowed : 0.58 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.15), residues: 3111 helix: -0.18 (0.29), residues: 360 sheet: 0.45 (0.17), residues: 1023 loop : -0.85 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 327 TYR 0.007 0.001 TYR N 49 PHE 0.008 0.001 PHE G 383 TRP 0.012 0.001 TRP A 631 HIS 0.005 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00538 (28103) covalent geometry : angle 0.75874 (38231) SS BOND : bond 0.00337 ( 48) SS BOND : angle 1.03793 ( 96) hydrogen bonds : bond 0.25999 ( 710) hydrogen bonds : angle 8.79486 ( 1827) link_ALPHA1-2 : bond 0.00161 ( 6) link_ALPHA1-2 : angle 2.18201 ( 18) link_ALPHA1-3 : bond 0.00419 ( 24) link_ALPHA1-3 : angle 2.10735 ( 72) link_ALPHA1-6 : bond 0.00349 ( 27) link_ALPHA1-6 : angle 1.82793 ( 81) link_BETA1-4 : bond 0.00386 ( 59) link_BETA1-4 : angle 1.43916 ( 177) link_BETA1-6 : bond 0.00553 ( 3) link_BETA1-6 : angle 1.44094 ( 9) link_NAG-ASN : bond 0.00281 ( 75) link_NAG-ASN : angle 1.87344 ( 225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 433 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 405 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7332 (p0) REVERT: G 464 ASP cc_start: 0.7291 (m-30) cc_final: 0.6864 (m-30) REVERT: S 98 ASP cc_start: 0.8528 (m-30) cc_final: 0.8012 (t0) REVERT: A 601 LYS cc_start: 0.8781 (mttp) cc_final: 0.8527 (mttm) REVERT: C 396 ILE cc_start: 0.7953 (tp) cc_final: 0.7718 (tp) REVERT: D 23 GLU cc_start: 0.7732 (tt0) cc_final: 0.7503 (tt0) REVERT: D 98 ASP cc_start: 0.8436 (m-30) cc_final: 0.8056 (t0) REVERT: F 79 GLN cc_start: 0.7728 (mt0) cc_final: 0.7385 (tm-30) REVERT: F 82 ASP cc_start: 0.8061 (t0) cc_final: 0.7712 (t0) REVERT: K 100 MET cc_start: 0.9147 (mtp) cc_final: 0.8916 (mtm) REVERT: K 397 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7471 (t0) REVERT: N 77 ASN cc_start: 0.7276 (t0) cc_final: 0.6910 (t0) REVERT: N 79 GLN cc_start: 0.7206 (mm110) cc_final: 0.6998 (mm110) outliers start: 6 outliers final: 3 residues processed: 439 average time/residue: 0.8155 time to fit residues: 408.6841 Evaluate side-chains 294 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 289 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 405 ASN Chi-restraints excluded: chain G residue 474 ASN Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 405 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0060 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 5.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 653 GLN G 67 ASN G 146 ASN G 183 GLN S 46 GLN L 6 GLN H 56 HIS H 96 HIS H 99 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN D 64 GLN E 26 ASN I 105 GLN K 258 GLN M 6 GLN M 39 GLN N 26 ASN N 38 GLN P 96 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.113515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.077248 restraints weight = 46736.556| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.17 r_work: 0.2932 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28345 Z= 0.132 Angle : 0.655 11.737 38909 Z= 0.314 Chirality : 0.047 0.373 4804 Planarity : 0.004 0.043 4598 Dihedral : 13.492 106.008 7333 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.53 % Favored : 94.37 % Rotamer: Outliers : 2.10 % Allowed : 8.98 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.16), residues: 3111 helix: 0.93 (0.29), residues: 342 sheet: 0.58 (0.17), residues: 993 loop : -0.73 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 166 TYR 0.013 0.001 TYR N 36 PHE 0.010 0.001 PHE F 71 TRP 0.014 0.001 TRP S 50 HIS 0.002 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00294 (28103) covalent geometry : angle 0.61373 (38231) SS BOND : bond 0.00516 ( 48) SS BOND : angle 1.13596 ( 96) hydrogen bonds : bond 0.05214 ( 710) hydrogen bonds : angle 5.88510 ( 1827) link_ALPHA1-2 : bond 0.00453 ( 6) link_ALPHA1-2 : angle 1.85522 ( 18) link_ALPHA1-3 : bond 0.00922 ( 24) link_ALPHA1-3 : angle 2.88173 ( 72) link_ALPHA1-6 : bond 0.00514 ( 27) link_ALPHA1-6 : angle 1.79673 ( 81) link_BETA1-4 : bond 0.00408 ( 59) link_BETA1-4 : angle 1.72894 ( 177) link_BETA1-6 : bond 0.00607 ( 3) link_BETA1-6 : angle 1.02845 ( 9) link_NAG-ASN : bond 0.00199 ( 75) link_NAG-ASN : angle 1.79956 ( 225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 321 time to evaluate : 1.098 Fit side-chains REVERT: G 102 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8014 (mm-30) REVERT: G 164 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7573 (pm20) REVERT: G 186 ASN cc_start: 0.7933 (t0) cc_final: 0.7725 (t0) REVERT: G 373 MET cc_start: 0.8831 (mtm) cc_final: 0.8326 (mmm) REVERT: G 464 ASP cc_start: 0.7379 (m-30) cc_final: 0.6875 (m-30) REVERT: U 40 ARG cc_start: 0.8655 (mmm-85) cc_final: 0.8020 (tpp-160) REVERT: U 77 ASN cc_start: 0.6611 (t0) cc_final: 0.6194 (t0) REVERT: U 79 GLN cc_start: 0.6345 (mm110) cc_final: 0.6038 (mm110) REVERT: A 601 LYS cc_start: 0.8365 (mttp) cc_final: 0.8012 (mttm) REVERT: C 186 ASN cc_start: 0.7976 (t0) cc_final: 0.7758 (t0) REVERT: C 428 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7087 (mm-40) REVERT: D 23 GLU cc_start: 0.7400 (tt0) cc_final: 0.7081 (tt0) REVERT: D 98 ASP cc_start: 0.8406 (m-30) cc_final: 0.7791 (t0) REVERT: E 77 ASN cc_start: 0.6706 (t0) cc_final: 0.6100 (t0) REVERT: E 79 GLN cc_start: 0.6090 (mm110) cc_final: 0.5731 (mm110) REVERT: E 87 PHE cc_start: 0.6688 (m-10) cc_final: 0.6422 (m-10) REVERT: E 96 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: F 11 LEU cc_start: 0.8113 (mm) cc_final: 0.7779 (mp) REVERT: F 61 ARG cc_start: 0.6095 (ptt90) cc_final: 0.5711 (ptt90) REVERT: F 70 ARG cc_start: 0.7668 (mtp180) cc_final: 0.7311 (mtp85) REVERT: I 48 MET cc_start: 0.7595 (mtp) cc_final: 0.7316 (mtp) REVERT: J 584 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7531 (mt-10) REVERT: K 100 MET cc_start: 0.8683 (mtp) cc_final: 0.8329 (mtm) REVERT: K 186 ASN cc_start: 0.7919 (t0) cc_final: 0.7681 (t0) REVERT: K 397 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7714 (t0) REVERT: N 3 GLN cc_start: 0.7292 (mm-40) cc_final: 0.7036 (mm-40) REVERT: N 77 ASN cc_start: 0.6802 (t0) cc_final: 0.6367 (t0) REVERT: N 79 GLN cc_start: 0.6385 (mm110) cc_final: 0.6151 (mm110) REVERT: O 27 GLN cc_start: 0.7606 (tm-30) cc_final: 0.6723 (tm-30) REVERT: O 28 ASP cc_start: 0.7879 (t70) cc_final: 0.7523 (t70) REVERT: O 79 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6853 (tm-30) REVERT: P 3 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6851 (t80) outliers start: 58 outliers final: 24 residues processed: 360 average time/residue: 0.7081 time to fit residues: 293.2510 Evaluate side-chains 315 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 284 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 80 MET Chi-restraints excluded: chain P residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 3 optimal weight: 10.0000 chunk 267 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN G 146 ASN U 79 GLN H 82BASN C 67 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN D 6 GLN E 26 ASN E 37 GLN E 79 GLN I 105 GLN J 577 GLN K 61 HIS K 67 ASN K 146 ASN M 39 GLN N 26 ASN P 96 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.111429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.075214 restraints weight = 47252.797| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.16 r_work: 0.2890 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28345 Z= 0.212 Angle : 0.690 14.028 38909 Z= 0.328 Chirality : 0.048 0.351 4804 Planarity : 0.004 0.043 4598 Dihedral : 12.434 98.927 7325 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.92 % Rotamer: Outliers : 3.29 % Allowed : 10.13 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.15), residues: 3111 helix: 0.93 (0.29), residues: 342 sheet: 0.45 (0.17), residues: 993 loop : -0.84 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 103 TYR 0.014 0.001 TYR E 49 PHE 0.013 0.001 PHE G 383 TRP 0.014 0.002 TRP S 50 HIS 0.004 0.001 HIS K 66 Details of bonding type rmsd covalent geometry : bond 0.00521 (28103) covalent geometry : angle 0.64404 (38231) SS BOND : bond 0.00695 ( 48) SS BOND : angle 1.67901 ( 96) hydrogen bonds : bond 0.05136 ( 710) hydrogen bonds : angle 5.47320 ( 1827) link_ALPHA1-2 : bond 0.00432 ( 6) link_ALPHA1-2 : angle 1.91064 ( 18) link_ALPHA1-3 : bond 0.00940 ( 24) link_ALPHA1-3 : angle 2.72409 ( 72) link_ALPHA1-6 : bond 0.00500 ( 27) link_ALPHA1-6 : angle 1.80758 ( 81) link_BETA1-4 : bond 0.00447 ( 59) link_BETA1-4 : angle 1.72652 ( 177) link_BETA1-6 : bond 0.00586 ( 3) link_BETA1-6 : angle 1.10709 ( 9) link_NAG-ASN : bond 0.00364 ( 75) link_NAG-ASN : angle 2.07584 ( 225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 302 time to evaluate : 1.079 Fit side-chains REVERT: G 102 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: G 186 ASN cc_start: 0.8119 (t0) cc_final: 0.7895 (t0) REVERT: G 428 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7325 (mm-40) REVERT: G 464 ASP cc_start: 0.7419 (m-30) cc_final: 0.6931 (m-30) REVERT: U 40 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8153 (tpp-160) REVERT: U 77 ASN cc_start: 0.6648 (t0) cc_final: 0.6188 (t0) REVERT: U 79 GLN cc_start: 0.6379 (mm-40) cc_final: 0.5967 (mm110) REVERT: H 3 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: A 601 LYS cc_start: 0.8390 (mttp) cc_final: 0.8020 (mttm) REVERT: C 80 ASN cc_start: 0.8338 (t0) cc_final: 0.8136 (t0) REVERT: C 164 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7959 (pm20) REVERT: C 186 ASN cc_start: 0.8087 (t0) cc_final: 0.7854 (t0) REVERT: C 428 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7088 (mm-40) REVERT: D 23 GLU cc_start: 0.7556 (tt0) cc_final: 0.7148 (tt0) REVERT: D 86 ASP cc_start: 0.8785 (m-30) cc_final: 0.8551 (m-30) REVERT: D 98 ASP cc_start: 0.8456 (m-30) cc_final: 0.7804 (t0) REVERT: D 100 ASP cc_start: 0.8301 (m-30) cc_final: 0.7887 (p0) REVERT: E 77 ASN cc_start: 0.6986 (t0) cc_final: 0.6421 (t0) REVERT: E 79 GLN cc_start: 0.6392 (mm-40) cc_final: 0.5925 (mm110) REVERT: E 96 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7927 (pm20) REVERT: F 70 ARG cc_start: 0.7827 (mtp180) cc_final: 0.7582 (mtp85) REVERT: I 26 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7919 (mtp85) REVERT: I 66 ARG cc_start: 0.5737 (OUTLIER) cc_final: 0.3941 (mtp180) REVERT: I 72 ASP cc_start: 0.7371 (t0) cc_final: 0.7018 (t70) REVERT: J 584 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7537 (mt-10) REVERT: K 100 MET cc_start: 0.8724 (mtp) cc_final: 0.8391 (mtm) REVERT: K 102 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8125 (mm-30) REVERT: K 186 ASN cc_start: 0.8037 (t0) cc_final: 0.7819 (t0) REVERT: K 397 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7800 (t0) REVERT: N 3 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6760 (mm-40) REVERT: N 77 ASN cc_start: 0.6875 (t0) cc_final: 0.6415 (t0) REVERT: N 79 GLN cc_start: 0.6205 (mm110) cc_final: 0.5956 (mm110) REVERT: O 27 GLN cc_start: 0.7654 (tm-30) cc_final: 0.6668 (tm-30) REVERT: O 79 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: P 3 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6824 (t80) outliers start: 91 outliers final: 42 residues processed: 360 average time/residue: 0.6938 time to fit residues: 289.1091 Evaluate side-chains 343 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 290 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 428 GLN Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 475 ILE Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 83 ARG Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 74 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 272 optimal weight: 5.9990 chunk 243 optimal weight: 0.3980 chunk 242 optimal weight: 0.6980 chunk 213 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 116 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 288 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN U 26 ASN H 96 HIS C 143 ASN C 146 ASN C 183 GLN D 6 GLN D 28 ASN E 3 GLN E 26 ASN I 105 GLN K 146 ASN M 39 GLN N 26 ASN P 96 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.113538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.077619 restraints weight = 46902.390| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.17 r_work: 0.2940 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28345 Z= 0.115 Angle : 0.617 10.609 38909 Z= 0.293 Chirality : 0.046 0.345 4804 Planarity : 0.004 0.042 4598 Dihedral : 11.416 94.637 7325 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.86 % Rotamer: Outliers : 2.50 % Allowed : 11.69 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.15), residues: 3111 helix: 1.42 (0.29), residues: 342 sheet: 0.61 (0.17), residues: 978 loop : -0.76 (0.15), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 103 TYR 0.013 0.001 TYR L 3 PHE 0.008 0.001 PHE F 94 TRP 0.013 0.001 TRP S 50 HIS 0.001 0.000 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00253 (28103) covalent geometry : angle 0.57813 (38231) SS BOND : bond 0.00460 ( 48) SS BOND : angle 1.04714 ( 96) hydrogen bonds : bond 0.03981 ( 710) hydrogen bonds : angle 5.09124 ( 1827) link_ALPHA1-2 : bond 0.00460 ( 6) link_ALPHA1-2 : angle 1.70624 ( 18) link_ALPHA1-3 : bond 0.01103 ( 24) link_ALPHA1-3 : angle 2.69564 ( 72) link_ALPHA1-6 : bond 0.00641 ( 27) link_ALPHA1-6 : angle 1.75525 ( 81) link_BETA1-4 : bond 0.00419 ( 59) link_BETA1-4 : angle 1.48745 ( 177) link_BETA1-6 : bond 0.00627 ( 3) link_BETA1-6 : angle 1.05113 ( 9) link_NAG-ASN : bond 0.00199 ( 75) link_NAG-ASN : angle 1.77276 ( 225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 1.023 Fit side-chains REVERT: G 102 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: G 164 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7530 (pm20) REVERT: G 186 ASN cc_start: 0.8087 (t0) cc_final: 0.7806 (t0) REVERT: G 464 ASP cc_start: 0.7381 (m-30) cc_final: 0.6878 (m-30) REVERT: S 83 ARG cc_start: 0.6883 (mpp80) cc_final: 0.6524 (mpp80) REVERT: S 86 ASP cc_start: 0.8736 (m-30) cc_final: 0.8332 (m-30) REVERT: U 26 ASN cc_start: 0.7720 (t0) cc_final: 0.7440 (t0) REVERT: U 40 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.8143 (tpp-160) REVERT: U 65 ARG cc_start: 0.7103 (ptm-80) cc_final: 0.6858 (ptm-80) REVERT: U 77 ASN cc_start: 0.6982 (t0) cc_final: 0.6496 (t0) REVERT: U 79 GLN cc_start: 0.6357 (mm-40) cc_final: 0.5870 (mm110) REVERT: H 3 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: C 80 ASN cc_start: 0.8353 (t0) cc_final: 0.8139 (t0) REVERT: C 186 ASN cc_start: 0.8121 (t0) cc_final: 0.7826 (t0) REVERT: C 396 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7451 (tp) REVERT: C 428 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7108 (mm-40) REVERT: D 23 GLU cc_start: 0.7502 (tt0) cc_final: 0.7110 (tt0) REVERT: D 86 ASP cc_start: 0.8669 (m-30) cc_final: 0.8301 (m-30) REVERT: D 98 ASP cc_start: 0.8410 (m-30) cc_final: 0.7780 (t0) REVERT: D 100 ASP cc_start: 0.8221 (m-30) cc_final: 0.7964 (p0) REVERT: E 77 ASN cc_start: 0.7179 (t0) cc_final: 0.6577 (t0) REVERT: E 79 GLN cc_start: 0.6173 (mm-40) cc_final: 0.5732 (mm110) REVERT: I 26 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7805 (mtp85) REVERT: I 72 ASP cc_start: 0.7290 (t0) cc_final: 0.6926 (t70) REVERT: J 584 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7501 (mt-10) REVERT: K 100 MET cc_start: 0.8632 (mtp) cc_final: 0.8345 (mtm) REVERT: K 102 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8101 (mm-30) REVERT: K 186 ASN cc_start: 0.8096 (t0) cc_final: 0.7849 (t0) REVERT: K 397 ASN cc_start: 0.8157 (OUTLIER) cc_final: 0.7882 (t0) REVERT: M 28 ASN cc_start: 0.8147 (p0) cc_final: 0.7513 (p0) REVERT: M 86 ASP cc_start: 0.8662 (m-30) cc_final: 0.8239 (m-30) REVERT: M 100 ASP cc_start: 0.7890 (m-30) cc_final: 0.7642 (OUTLIER) REVERT: N 3 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6634 (mm-40) REVERT: N 77 ASN cc_start: 0.6897 (t0) cc_final: 0.6227 (t0) REVERT: N 79 GLN cc_start: 0.6266 (mm110) cc_final: 0.5841 (mm110) REVERT: O 27 GLN cc_start: 0.7710 (tm-30) cc_final: 0.6687 (tm-30) REVERT: O 28 ASP cc_start: 0.7884 (t70) cc_final: 0.7543 (t0) REVERT: O 79 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6789 (tm-30) REVERT: P 3 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6740 (t80) outliers start: 69 outliers final: 35 residues processed: 358 average time/residue: 0.7186 time to fit residues: 297.6404 Evaluate side-chains 335 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 240 optimal weight: 0.0670 chunk 147 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 66 optimal weight: 0.0060 chunk 297 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 overall best weight: 1.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 80 ASN G 146 ASN S 28 ASN H 96 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN C 428 GLN D 6 GLN D 28 ASN E 26 ASN I 105 GLN K 146 ASN M 39 GLN N 26 ASN O 6 GLN P 96 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.111721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.075563 restraints weight = 46858.201| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.16 r_work: 0.2901 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 28345 Z= 0.185 Angle : 0.662 10.877 38909 Z= 0.311 Chirality : 0.047 0.349 4804 Planarity : 0.004 0.043 4598 Dihedral : 11.077 90.164 7325 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.92 % Rotamer: Outliers : 3.08 % Allowed : 12.45 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.15), residues: 3111 helix: 1.32 (0.29), residues: 342 sheet: 0.50 (0.16), residues: 1032 loop : -0.80 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 40 TYR 0.014 0.001 TYR E 49 PHE 0.012 0.001 PHE G 383 TRP 0.013 0.001 TRP S 50 HIS 0.003 0.001 HIS G 375 Details of bonding type rmsd covalent geometry : bond 0.00450 (28103) covalent geometry : angle 0.61934 (38231) SS BOND : bond 0.00520 ( 48) SS BOND : angle 1.22295 ( 96) hydrogen bonds : bond 0.04380 ( 710) hydrogen bonds : angle 5.01377 ( 1827) link_ALPHA1-2 : bond 0.00392 ( 6) link_ALPHA1-2 : angle 1.83753 ( 18) link_ALPHA1-3 : bond 0.01003 ( 24) link_ALPHA1-3 : angle 2.79051 ( 72) link_ALPHA1-6 : bond 0.00579 ( 27) link_ALPHA1-6 : angle 1.77039 ( 81) link_BETA1-4 : bond 0.00425 ( 59) link_BETA1-4 : angle 1.57301 ( 177) link_BETA1-6 : bond 0.00590 ( 3) link_BETA1-6 : angle 1.09771 ( 9) link_NAG-ASN : bond 0.00318 ( 75) link_NAG-ASN : angle 1.99613 ( 225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 306 time to evaluate : 0.849 Fit side-chains REVERT: G 102 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: G 164 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: G 186 ASN cc_start: 0.8235 (t0) cc_final: 0.7972 (t0) REVERT: G 464 ASP cc_start: 0.7400 (m-30) cc_final: 0.6910 (m-30) REVERT: S 83 ARG cc_start: 0.6966 (mpp80) cc_final: 0.6581 (mpp80) REVERT: S 86 ASP cc_start: 0.8749 (m-30) cc_final: 0.8370 (m-30) REVERT: U 26 ASN cc_start: 0.7826 (t0) cc_final: 0.7471 (t0) REVERT: U 77 ASN cc_start: 0.6972 (t0) cc_final: 0.6542 (t0) REVERT: U 79 GLN cc_start: 0.6333 (mm-40) cc_final: 0.5960 (mm110) REVERT: H 3 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: A 530 MET cc_start: 0.8008 (mtt) cc_final: 0.7434 (mtt) REVERT: C 80 ASN cc_start: 0.8401 (t0) cc_final: 0.8152 (t0) REVERT: C 164 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7796 (pm20) REVERT: C 186 ASN cc_start: 0.8170 (t0) cc_final: 0.7868 (t0) REVERT: D 23 GLU cc_start: 0.7660 (tt0) cc_final: 0.7230 (tt0) REVERT: D 83 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6459 (mtp180) REVERT: D 86 ASP cc_start: 0.8683 (m-30) cc_final: 0.8386 (m-30) REVERT: D 98 ASP cc_start: 0.8459 (m-30) cc_final: 0.7794 (t0) REVERT: D 100 ASP cc_start: 0.8270 (m-30) cc_final: 0.7906 (p0) REVERT: E 77 ASN cc_start: 0.7321 (t0) cc_final: 0.6772 (t0) REVERT: E 79 GLN cc_start: 0.6428 (mm-40) cc_final: 0.6006 (mm110) REVERT: E 96 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: F 82 ASP cc_start: 0.7608 (t0) cc_final: 0.7129 (m-30) REVERT: I 26 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7831 (mtp85) REVERT: I 72 ASP cc_start: 0.7329 (t0) cc_final: 0.6916 (t70) REVERT: I 82 ASN cc_start: 0.6393 (t0) cc_final: 0.6043 (t0) REVERT: J 584 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7615 (mt-10) REVERT: K 100 MET cc_start: 0.8649 (mtp) cc_final: 0.8347 (mtm) REVERT: K 102 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: K 186 ASN cc_start: 0.8120 (t0) cc_final: 0.7876 (t0) REVERT: K 397 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7955 (t0) REVERT: M 28 ASN cc_start: 0.8203 (p0) cc_final: 0.7561 (p0) REVERT: M 74 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8668 (m-30) REVERT: N 3 GLN cc_start: 0.7350 (mm-40) cc_final: 0.6720 (mm-40) REVERT: N 77 ASN cc_start: 0.6983 (t0) cc_final: 0.6640 (t0) REVERT: N 79 GLN cc_start: 0.6269 (mm110) cc_final: 0.6001 (mm110) REVERT: O 27 GLN cc_start: 0.7818 (tm-30) cc_final: 0.6792 (tm-30) REVERT: O 79 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: P 3 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6796 (t80) REVERT: P 26 ARG cc_start: 0.7482 (mtm110) cc_final: 0.7124 (mtp-110) outliers start: 85 outliers final: 44 residues processed: 354 average time/residue: 0.7039 time to fit residues: 287.9697 Evaluate side-chains 349 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 294 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 428 GLN Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 228 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 174 optimal weight: 0.0470 chunk 220 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 260 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN H 96 HIS A 575 GLN ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN D 6 GLN E 3 GLN E 26 ASN I 105 GLN K 146 ASN M 39 GLN N 26 ASN P 96 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.113249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.077315 restraints weight = 46720.803| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.16 r_work: 0.2933 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28345 Z= 0.116 Angle : 0.617 9.496 38909 Z= 0.290 Chirality : 0.046 0.345 4804 Planarity : 0.004 0.041 4598 Dihedral : 10.527 89.307 7325 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.34 % Favored : 94.57 % Rotamer: Outliers : 2.57 % Allowed : 13.61 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 3111 helix: 1.63 (0.29), residues: 342 sheet: 0.54 (0.16), residues: 1032 loop : -0.75 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 103 TYR 0.014 0.001 TYR L 3 PHE 0.007 0.001 PHE K 383 TRP 0.013 0.001 TRP D 50 HIS 0.001 0.000 HIS J 564 Details of bonding type rmsd covalent geometry : bond 0.00260 (28103) covalent geometry : angle 0.57888 (38231) SS BOND : bond 0.00421 ( 48) SS BOND : angle 0.92806 ( 96) hydrogen bonds : bond 0.03782 ( 710) hydrogen bonds : angle 4.83030 ( 1827) link_ALPHA1-2 : bond 0.00410 ( 6) link_ALPHA1-2 : angle 1.71882 ( 18) link_ALPHA1-3 : bond 0.01156 ( 24) link_ALPHA1-3 : angle 2.71477 ( 72) link_ALPHA1-6 : bond 0.00666 ( 27) link_ALPHA1-6 : angle 1.73787 ( 81) link_BETA1-4 : bond 0.00417 ( 59) link_BETA1-4 : angle 1.43573 ( 177) link_BETA1-6 : bond 0.00610 ( 3) link_BETA1-6 : angle 1.06762 ( 9) link_NAG-ASN : bond 0.00187 ( 75) link_NAG-ASN : angle 1.80236 ( 225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 308 time to evaluate : 1.007 Fit side-chains REVERT: G 102 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8067 (mm-30) REVERT: G 164 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: G 186 ASN cc_start: 0.8080 (t0) cc_final: 0.7784 (t0) REVERT: G 464 ASP cc_start: 0.7385 (m-30) cc_final: 0.6901 (m-30) REVERT: S 5 LEU cc_start: 0.7585 (mp) cc_final: 0.7297 (mt) REVERT: S 83 ARG cc_start: 0.6913 (mpp80) cc_final: 0.6556 (mpp80) REVERT: S 86 ASP cc_start: 0.8676 (m-30) cc_final: 0.8245 (m-30) REVERT: S 100 ASP cc_start: 0.7957 (m-30) cc_final: 0.7545 (p0) REVERT: U 26 ASN cc_start: 0.7849 (t0) cc_final: 0.7550 (t0) REVERT: U 40 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8068 (tpp-160) REVERT: U 77 ASN cc_start: 0.7114 (t0) cc_final: 0.6668 (t0) REVERT: U 79 GLN cc_start: 0.6342 (mm-40) cc_final: 0.5882 (mm110) REVERT: L 70 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7311 (mmm-85) REVERT: H 3 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6612 (m-80) REVERT: A 530 MET cc_start: 0.8023 (mtt) cc_final: 0.7542 (mtt) REVERT: C 80 ASN cc_start: 0.8401 (t0) cc_final: 0.8143 (t0) REVERT: C 164 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: C 186 ASN cc_start: 0.8135 (t0) cc_final: 0.7889 (t0) REVERT: D 23 GLU cc_start: 0.7535 (tt0) cc_final: 0.7106 (tt0) REVERT: D 83 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6389 (mtp180) REVERT: D 86 ASP cc_start: 0.8574 (m-30) cc_final: 0.8207 (m-30) REVERT: D 98 ASP cc_start: 0.8420 (m-30) cc_final: 0.7807 (t0) REVERT: E 77 ASN cc_start: 0.7309 (t0) cc_final: 0.6759 (t0) REVERT: E 79 GLN cc_start: 0.6169 (mm-40) cc_final: 0.5765 (mm110) REVERT: E 96 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7859 (pm20) REVERT: F 82 ASP cc_start: 0.7499 (t0) cc_final: 0.6900 (m-30) REVERT: I 26 ARG cc_start: 0.8133 (mtp85) cc_final: 0.7787 (mtp85) REVERT: I 72 ASP cc_start: 0.7248 (t0) cc_final: 0.6863 (t70) REVERT: I 82 ASN cc_start: 0.6393 (t0) cc_final: 0.6040 (t0) REVERT: K 100 MET cc_start: 0.8604 (mtp) cc_final: 0.8376 (mtm) REVERT: K 102 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8108 (mm-30) REVERT: K 186 ASN cc_start: 0.8165 (t0) cc_final: 0.7914 (t0) REVERT: K 397 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7892 (t0) REVERT: M 28 ASN cc_start: 0.8102 (p0) cc_final: 0.7350 (p0) REVERT: M 74 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8004 (p0) REVERT: N 3 GLN cc_start: 0.7353 (mm-40) cc_final: 0.6686 (mm-40) REVERT: N 65 ARG cc_start: 0.6450 (ptm160) cc_final: 0.6249 (ptm160) REVERT: N 77 ASN cc_start: 0.6956 (t0) cc_final: 0.6623 (t0) REVERT: N 79 GLN cc_start: 0.6285 (mm110) cc_final: 0.6011 (mm110) REVERT: O 27 GLN cc_start: 0.7835 (tm-30) cc_final: 0.6882 (tm-30) REVERT: O 79 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6756 (tm-30) REVERT: O 82 ASP cc_start: 0.7179 (m-30) cc_final: 0.6735 (m-30) REVERT: P 3 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6749 (t80) REVERT: P 26 ARG cc_start: 0.7449 (mtm110) cc_final: 0.7104 (mtp-110) outliers start: 71 outliers final: 37 residues processed: 350 average time/residue: 0.7551 time to fit residues: 304.8935 Evaluate side-chains 347 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 299 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 74 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 63 optimal weight: 4.9990 chunk 251 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 175 optimal weight: 9.9990 chunk 243 optimal weight: 0.0670 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 190 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN H 96 HIS ** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN C 183 GLN D 6 GLN D 28 ASN E 26 ASN I 105 GLN K 146 ASN M 39 GLN N 26 ASN P 96 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.113312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.077409 restraints weight = 46647.291| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.17 r_work: 0.2938 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28345 Z= 0.122 Angle : 0.621 9.158 38909 Z= 0.292 Chirality : 0.046 0.346 4804 Planarity : 0.004 0.045 4598 Dihedral : 10.217 87.189 7325 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 2.46 % Allowed : 14.12 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.15), residues: 3111 helix: 1.76 (0.29), residues: 342 sheet: 0.57 (0.16), residues: 1014 loop : -0.71 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 103 TYR 0.014 0.001 TYR O 3 PHE 0.008 0.001 PHE G 383 TRP 0.013 0.001 TRP S 50 HIS 0.001 0.000 HIS J 564 Details of bonding type rmsd covalent geometry : bond 0.00281 (28103) covalent geometry : angle 0.58366 (38231) SS BOND : bond 0.00460 ( 48) SS BOND : angle 0.99002 ( 96) hydrogen bonds : bond 0.03700 ( 710) hydrogen bonds : angle 4.74969 ( 1827) link_ALPHA1-2 : bond 0.00400 ( 6) link_ALPHA1-2 : angle 1.71340 ( 18) link_ALPHA1-3 : bond 0.01133 ( 24) link_ALPHA1-3 : angle 2.65281 ( 72) link_ALPHA1-6 : bond 0.00669 ( 27) link_ALPHA1-6 : angle 1.73222 ( 81) link_BETA1-4 : bond 0.00423 ( 59) link_BETA1-4 : angle 1.41750 ( 177) link_BETA1-6 : bond 0.00613 ( 3) link_BETA1-6 : angle 1.06286 ( 9) link_NAG-ASN : bond 0.00187 ( 75) link_NAG-ASN : angle 1.77453 ( 225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 305 time to evaluate : 1.131 Fit side-chains REVERT: G 102 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: G 164 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: G 186 ASN cc_start: 0.8148 (t0) cc_final: 0.7876 (t0) REVERT: G 464 ASP cc_start: 0.7375 (m-30) cc_final: 0.6889 (m-30) REVERT: S 5 LEU cc_start: 0.7590 (mp) cc_final: 0.7309 (mt) REVERT: S 83 ARG cc_start: 0.6894 (mpp80) cc_final: 0.6515 (mpp80) REVERT: S 86 ASP cc_start: 0.8627 (m-30) cc_final: 0.8142 (m-30) REVERT: S 100 ASP cc_start: 0.7902 (m-30) cc_final: 0.7619 (p0) REVERT: U 26 ASN cc_start: 0.7825 (t0) cc_final: 0.7562 (t0) REVERT: U 40 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.8030 (tpp-160) REVERT: U 61 ARG cc_start: 0.7084 (ttp-110) cc_final: 0.6647 (ttp-110) REVERT: U 77 ASN cc_start: 0.7112 (t0) cc_final: 0.6547 (t0) REVERT: U 79 GLN cc_start: 0.6330 (mm-40) cc_final: 0.5860 (mm110) REVERT: L 70 ARG cc_start: 0.7630 (mmm160) cc_final: 0.7300 (mmm-85) REVERT: H 3 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: H 82 ASN cc_start: 0.6581 (t0) cc_final: 0.6279 (t0) REVERT: A 657 GLU cc_start: 0.8195 (tt0) cc_final: 0.7809 (tt0) REVERT: C 80 ASN cc_start: 0.8406 (t0) cc_final: 0.8147 (t0) REVERT: C 164 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: C 186 ASN cc_start: 0.8087 (t0) cc_final: 0.7725 (t0) REVERT: D 23 GLU cc_start: 0.7529 (tt0) cc_final: 0.7095 (tt0) REVERT: D 83 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6394 (mtp180) REVERT: D 86 ASP cc_start: 0.8557 (m-30) cc_final: 0.8147 (m-30) REVERT: D 98 ASP cc_start: 0.8406 (m-30) cc_final: 0.7819 (t0) REVERT: D 100 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7839 (p0) REVERT: E 77 ASN cc_start: 0.7309 (t0) cc_final: 0.6758 (t0) REVERT: E 79 GLN cc_start: 0.6148 (mm-40) cc_final: 0.5745 (mm110) REVERT: E 96 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: F 11 LEU cc_start: 0.7765 (mm) cc_final: 0.7560 (mp) REVERT: F 82 ASP cc_start: 0.7438 (t0) cc_final: 0.6811 (m-30) REVERT: I 26 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7811 (mtp85) REVERT: I 72 ASP cc_start: 0.7233 (t0) cc_final: 0.6821 (t70) REVERT: I 82 ASN cc_start: 0.6533 (t0) cc_final: 0.6218 (t0) REVERT: J 584 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7340 (mt-10) REVERT: K 100 MET cc_start: 0.8567 (mtp) cc_final: 0.8303 (mtm) REVERT: K 102 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8038 (mm-30) REVERT: K 186 ASN cc_start: 0.8149 (t0) cc_final: 0.7889 (t0) REVERT: K 397 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7885 (t0) REVERT: M 28 ASN cc_start: 0.7955 (p0) cc_final: 0.7323 (p0) REVERT: M 74 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8009 (p0) REVERT: M 100 ASP cc_start: 0.8003 (p0) cc_final: 0.7772 (p0) REVERT: N 3 GLN cc_start: 0.7389 (mm-40) cc_final: 0.6679 (mm-40) REVERT: N 40 ARG cc_start: 0.7927 (tpp80) cc_final: 0.7694 (tpp-160) REVERT: N 65 ARG cc_start: 0.6371 (ptm160) cc_final: 0.6147 (ptm160) REVERT: N 77 ASN cc_start: 0.6943 (t0) cc_final: 0.6619 (t0) REVERT: N 79 GLN cc_start: 0.6341 (mm110) cc_final: 0.6078 (mm110) REVERT: O 27 GLN cc_start: 0.7837 (tm-30) cc_final: 0.6865 (tm-30) REVERT: O 70 ARG cc_start: 0.7405 (mtp85) cc_final: 0.7091 (mtm110) REVERT: O 79 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.6674 (tm-30) REVERT: O 82 ASP cc_start: 0.7019 (m-30) cc_final: 0.6783 (m-30) REVERT: P 3 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6682 (t80) REVERT: P 26 ARG cc_start: 0.7439 (mtm110) cc_final: 0.7083 (mtp-110) outliers start: 68 outliers final: 39 residues processed: 345 average time/residue: 0.7561 time to fit residues: 301.1235 Evaluate side-chains 352 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 301 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 184 MET Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 6 optimal weight: 0.9980 chunk 217 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 0.0020 chunk 287 optimal weight: 7.9990 chunk 246 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 overall best weight: 0.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN H 96 HIS A 577 GLN C 146 ASN C 183 GLN C 258 GLN D 6 GLN D 28 ASN E 3 GLN E 26 ASN I 105 GLN K 146 ASN N 26 ASN P 96 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.114407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.078988 restraints weight = 46731.740| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.12 r_work: 0.2959 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28345 Z= 0.113 Angle : 0.606 8.334 38909 Z= 0.285 Chirality : 0.045 0.347 4804 Planarity : 0.004 0.039 4598 Dihedral : 9.657 83.230 7325 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.70 % Rotamer: Outliers : 2.14 % Allowed : 14.95 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.16), residues: 3111 helix: 1.91 (0.29), residues: 342 sheet: 0.51 (0.16), residues: 1038 loop : -0.62 (0.16), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 103 TYR 0.018 0.001 TYR L 3 PHE 0.008 0.001 PHE C 383 TRP 0.014 0.001 TRP B 571 HIS 0.001 0.000 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00254 (28103) covalent geometry : angle 0.57106 (38231) SS BOND : bond 0.00420 ( 48) SS BOND : angle 0.89594 ( 96) hydrogen bonds : bond 0.03489 ( 710) hydrogen bonds : angle 4.60852 ( 1827) link_ALPHA1-2 : bond 0.00409 ( 6) link_ALPHA1-2 : angle 1.67284 ( 18) link_ALPHA1-3 : bond 0.01149 ( 24) link_ALPHA1-3 : angle 2.57134 ( 72) link_ALPHA1-6 : bond 0.00715 ( 27) link_ALPHA1-6 : angle 1.70357 ( 81) link_BETA1-4 : bond 0.00448 ( 59) link_BETA1-4 : angle 1.35372 ( 177) link_BETA1-6 : bond 0.00610 ( 3) link_BETA1-6 : angle 1.05285 ( 9) link_NAG-ASN : bond 0.00175 ( 75) link_NAG-ASN : angle 1.69620 ( 225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 317 time to evaluate : 1.099 Fit side-chains REVERT: G 102 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: G 164 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: G 186 ASN cc_start: 0.8023 (t0) cc_final: 0.7718 (t0) REVERT: G 464 ASP cc_start: 0.7354 (m-30) cc_final: 0.6876 (m-30) REVERT: S 5 LEU cc_start: 0.7682 (mp) cc_final: 0.7385 (mt) REVERT: S 83 ARG cc_start: 0.6858 (mpp80) cc_final: 0.6470 (mpp80) REVERT: S 86 ASP cc_start: 0.8668 (m-30) cc_final: 0.8203 (m-30) REVERT: U 61 ARG cc_start: 0.7056 (ttp-110) cc_final: 0.6669 (ttp-110) REVERT: U 77 ASN cc_start: 0.7147 (t0) cc_final: 0.6570 (t0) REVERT: U 79 GLN cc_start: 0.6489 (mm-40) cc_final: 0.6029 (mm110) REVERT: L 70 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7286 (mmm-85) REVERT: H 3 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: H 82 ASN cc_start: 0.6688 (t0) cc_final: 0.6388 (t0) REVERT: A 657 GLU cc_start: 0.8215 (tt0) cc_final: 0.7833 (tt0) REVERT: C 80 ASN cc_start: 0.8431 (t0) cc_final: 0.8164 (t0) REVERT: C 164 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: C 186 ASN cc_start: 0.8062 (t0) cc_final: 0.7728 (t0) REVERT: D 23 GLU cc_start: 0.7602 (tt0) cc_final: 0.7172 (tt0) REVERT: D 83 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6444 (mtp180) REVERT: D 86 ASP cc_start: 0.8428 (m-30) cc_final: 0.8028 (m-30) REVERT: D 98 ASP cc_start: 0.8385 (m-30) cc_final: 0.7852 (t0) REVERT: E 26 ASN cc_start: 0.7861 (t0) cc_final: 0.7493 (t0) REVERT: E 77 ASN cc_start: 0.7397 (t0) cc_final: 0.6864 (t0) REVERT: E 79 GLN cc_start: 0.6232 (mm-40) cc_final: 0.5804 (mm110) REVERT: F 82 ASP cc_start: 0.7491 (t0) cc_final: 0.6786 (m-30) REVERT: I 26 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7955 (mtp85) REVERT: I 72 ASP cc_start: 0.7286 (t0) cc_final: 0.6891 (t70) REVERT: I 82 ASN cc_start: 0.6749 (t0) cc_final: 0.6466 (t0) REVERT: K 100 MET cc_start: 0.8585 (mtp) cc_final: 0.8376 (mtm) REVERT: K 102 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: K 186 ASN cc_start: 0.8160 (t0) cc_final: 0.7892 (t0) REVERT: K 397 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7946 (t0) REVERT: M 28 ASN cc_start: 0.7900 (p0) cc_final: 0.7297 (p0) REVERT: M 74 ASP cc_start: 0.8869 (m-30) cc_final: 0.8029 (p0) REVERT: N 3 GLN cc_start: 0.7456 (mm-40) cc_final: 0.6836 (mm-40) REVERT: N 77 ASN cc_start: 0.7068 (t0) cc_final: 0.6715 (t0) REVERT: N 79 GLN cc_start: 0.6421 (mm110) cc_final: 0.6087 (mm110) REVERT: O 27 GLN cc_start: 0.7860 (tm-30) cc_final: 0.6909 (tm-30) REVERT: O 70 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7066 (mtm110) REVERT: O 79 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6723 (tm-30) REVERT: P 3 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6574 (t80) REVERT: P 26 ARG cc_start: 0.7448 (mtm110) cc_final: 0.7090 (mtp-110) outliers start: 59 outliers final: 38 residues processed: 349 average time/residue: 0.6901 time to fit residues: 278.8262 Evaluate side-chains 348 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain K residue 426 MET Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 102 THR Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 286 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 299 optimal weight: 4.9990 chunk 184 optimal weight: 7.9990 chunk 194 optimal weight: 0.0030 chunk 142 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN H 82BASN H 96 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN D 6 GLN D 28 ASN I 105 GLN K 146 ASN N 26 ASN P 96 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.114108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.078661 restraints weight = 47013.516| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.12 r_work: 0.2953 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28345 Z= 0.121 Angle : 0.614 8.428 38909 Z= 0.289 Chirality : 0.045 0.347 4804 Planarity : 0.004 0.040 4598 Dihedral : 9.441 79.521 7325 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.46 % Favored : 94.44 % Rotamer: Outliers : 1.88 % Allowed : 15.45 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.16), residues: 3111 helix: 1.95 (0.29), residues: 342 sheet: 0.51 (0.16), residues: 1038 loop : -0.63 (0.16), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 103 TYR 0.018 0.001 TYR O 3 PHE 0.008 0.001 PHE G 383 TRP 0.017 0.001 TRP B 571 HIS 0.001 0.000 HIS J 564 Details of bonding type rmsd covalent geometry : bond 0.00278 (28103) covalent geometry : angle 0.57842 (38231) SS BOND : bond 0.00431 ( 48) SS BOND : angle 0.91931 ( 96) hydrogen bonds : bond 0.03547 ( 710) hydrogen bonds : angle 4.56250 ( 1827) link_ALPHA1-2 : bond 0.00380 ( 6) link_ALPHA1-2 : angle 1.68971 ( 18) link_ALPHA1-3 : bond 0.01135 ( 24) link_ALPHA1-3 : angle 2.60354 ( 72) link_ALPHA1-6 : bond 0.00712 ( 27) link_ALPHA1-6 : angle 1.69584 ( 81) link_BETA1-4 : bond 0.00444 ( 59) link_BETA1-4 : angle 1.36438 ( 177) link_BETA1-6 : bond 0.00588 ( 3) link_BETA1-6 : angle 1.07251 ( 9) link_NAG-ASN : bond 0.00182 ( 75) link_NAG-ASN : angle 1.72150 ( 225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 306 time to evaluate : 1.054 Fit side-chains REVERT: G 102 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: G 164 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: G 186 ASN cc_start: 0.8039 (t0) cc_final: 0.7732 (t0) REVERT: G 464 ASP cc_start: 0.7367 (m-30) cc_final: 0.6889 (m-30) REVERT: S 5 LEU cc_start: 0.7675 (mp) cc_final: 0.7377 (mt) REVERT: S 86 ASP cc_start: 0.8689 (m-30) cc_final: 0.8254 (m-30) REVERT: S 98 ASP cc_start: 0.8456 (m-30) cc_final: 0.7679 (t0) REVERT: U 40 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.7889 (tpp-160) REVERT: U 61 ARG cc_start: 0.7079 (ttp-110) cc_final: 0.6688 (ttp-110) REVERT: U 77 ASN cc_start: 0.7157 (t0) cc_final: 0.6617 (t0) REVERT: U 79 GLN cc_start: 0.6496 (mm-40) cc_final: 0.6030 (mm110) REVERT: L 24 ARG cc_start: 0.7066 (mtp-110) cc_final: 0.6612 (mtp-110) REVERT: L 70 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7273 (mmm-85) REVERT: H 3 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6501 (m-80) REVERT: H 82 ASN cc_start: 0.6722 (t0) cc_final: 0.6402 (t0) REVERT: A 657 GLU cc_start: 0.8223 (tt0) cc_final: 0.7838 (tt0) REVERT: C 80 ASN cc_start: 0.8433 (t0) cc_final: 0.8170 (t0) REVERT: C 164 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: C 186 ASN cc_start: 0.8063 (t0) cc_final: 0.7738 (t0) REVERT: D 5 LEU cc_start: 0.7866 (mp) cc_final: 0.7614 (mt) REVERT: D 23 GLU cc_start: 0.7569 (tt0) cc_final: 0.7123 (tt0) REVERT: D 83 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6440 (mtp180) REVERT: D 86 ASP cc_start: 0.8396 (m-30) cc_final: 0.8040 (m-30) REVERT: D 98 ASP cc_start: 0.8370 (m-30) cc_final: 0.7862 (t0) REVERT: E 77 ASN cc_start: 0.7400 (t0) cc_final: 0.6869 (t0) REVERT: E 79 GLN cc_start: 0.6246 (mm-40) cc_final: 0.5813 (mm110) REVERT: F 70 ARG cc_start: 0.7697 (mtp-110) cc_final: 0.7380 (mtp85) REVERT: F 82 ASP cc_start: 0.7480 (t0) cc_final: 0.6765 (m-30) REVERT: I 26 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7977 (mtp85) REVERT: I 72 ASP cc_start: 0.7357 (t0) cc_final: 0.6974 (t70) REVERT: I 82 ASN cc_start: 0.6754 (t0) cc_final: 0.6511 (t0) REVERT: K 50 THR cc_start: 0.8494 (t) cc_final: 0.8242 (t) REVERT: K 100 MET cc_start: 0.8567 (mtp) cc_final: 0.8311 (mtm) REVERT: K 102 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8080 (mm-30) REVERT: K 186 ASN cc_start: 0.8161 (t0) cc_final: 0.7904 (t0) REVERT: K 397 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7894 (t0) REVERT: M 28 ASN cc_start: 0.7881 (p0) cc_final: 0.7276 (p0) REVERT: M 74 ASP cc_start: 0.8864 (m-30) cc_final: 0.8035 (p0) REVERT: N 3 GLN cc_start: 0.7424 (mm-40) cc_final: 0.6680 (mm-40) REVERT: N 77 ASN cc_start: 0.7061 (t0) cc_final: 0.6733 (t0) REVERT: N 79 GLN cc_start: 0.6329 (mm110) cc_final: 0.5991 (mm110) REVERT: O 27 GLN cc_start: 0.7888 (tm-30) cc_final: 0.6910 (tm-30) REVERT: O 79 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: P 3 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6610 (t80) REVERT: P 26 ARG cc_start: 0.7281 (mtm110) cc_final: 0.7014 (mtp180) REVERT: P 66 ARG cc_start: 0.6348 (mtp180) cc_final: 0.5909 (ttp-110) outliers start: 52 outliers final: 37 residues processed: 335 average time/residue: 0.6724 time to fit residues: 259.6922 Evaluate side-chains 347 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 301 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 371 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 41 optimal weight: 0.8980 chunk 263 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 56 optimal weight: 0.0980 chunk 171 optimal weight: 0.7980 chunk 234 optimal weight: 0.0870 chunk 112 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN H 96 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN D 6 GLN D 28 ASN E 26 ASN K 146 ASN P 96 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.114220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078721 restraints weight = 46932.415| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.12 r_work: 0.2954 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28345 Z= 0.122 Angle : 0.804 59.199 38909 Z= 0.399 Chirality : 0.045 0.347 4804 Planarity : 0.004 0.056 4598 Dihedral : 9.434 79.401 7325 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.31 % Rotamer: Outliers : 1.66 % Allowed : 15.49 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.16), residues: 3111 helix: 1.96 (0.29), residues: 342 sheet: 0.51 (0.16), residues: 1038 loop : -0.63 (0.16), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 103 TYR 0.016 0.001 TYR G 173 PHE 0.007 0.001 PHE K 383 TRP 0.019 0.001 TRP B 571 HIS 0.001 0.000 HIS J 564 Details of bonding type rmsd covalent geometry : bond 0.00270 (28103) covalent geometry : angle 0.78081 (38231) SS BOND : bond 0.00419 ( 48) SS BOND : angle 0.89297 ( 96) hydrogen bonds : bond 0.03521 ( 710) hydrogen bonds : angle 4.55880 ( 1827) link_ALPHA1-2 : bond 0.00376 ( 6) link_ALPHA1-2 : angle 1.68993 ( 18) link_ALPHA1-3 : bond 0.01140 ( 24) link_ALPHA1-3 : angle 2.60124 ( 72) link_ALPHA1-6 : bond 0.00726 ( 27) link_ALPHA1-6 : angle 1.70082 ( 81) link_BETA1-4 : bond 0.00446 ( 59) link_BETA1-4 : angle 1.36127 ( 177) link_BETA1-6 : bond 0.00578 ( 3) link_BETA1-6 : angle 1.07985 ( 9) link_NAG-ASN : bond 0.00174 ( 75) link_NAG-ASN : angle 1.72226 ( 225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6222 Ramachandran restraints generated. 3111 Oldfield, 0 Emsley, 3111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 300 time to evaluate : 1.099 Fit side-chains REVERT: G 102 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: G 164 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: G 186 ASN cc_start: 0.8038 (t0) cc_final: 0.7731 (t0) REVERT: G 464 ASP cc_start: 0.7364 (m-30) cc_final: 0.6886 (m-30) REVERT: S 5 LEU cc_start: 0.7671 (mp) cc_final: 0.7374 (mt) REVERT: S 86 ASP cc_start: 0.8692 (m-30) cc_final: 0.8259 (m-30) REVERT: S 98 ASP cc_start: 0.8459 (m-30) cc_final: 0.7679 (t0) REVERT: U 40 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.7983 (tpp-160) REVERT: U 61 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6679 (ttp-110) REVERT: U 77 ASN cc_start: 0.7153 (t0) cc_final: 0.6613 (t0) REVERT: U 79 GLN cc_start: 0.6488 (mm-40) cc_final: 0.6024 (mm110) REVERT: L 24 ARG cc_start: 0.7065 (mtp-110) cc_final: 0.6522 (mtp-110) REVERT: L 70 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7129 (mmm-85) REVERT: H 3 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: H 26 ARG cc_start: 0.7792 (mtm-85) cc_final: 0.7373 (mtm110) REVERT: H 82 ASN cc_start: 0.6717 (t0) cc_final: 0.6395 (t0) REVERT: A 657 GLU cc_start: 0.8223 (tt0) cc_final: 0.7837 (tt0) REVERT: C 80 ASN cc_start: 0.8432 (t0) cc_final: 0.8168 (t0) REVERT: C 164 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: C 186 ASN cc_start: 0.8059 (t0) cc_final: 0.7733 (t0) REVERT: D 5 LEU cc_start: 0.7875 (mp) cc_final: 0.7621 (mt) REVERT: D 23 GLU cc_start: 0.7567 (tt0) cc_final: 0.7120 (tt0) REVERT: D 83 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6436 (mtp180) REVERT: D 86 ASP cc_start: 0.8394 (m-30) cc_final: 0.8037 (m-30) REVERT: D 98 ASP cc_start: 0.8369 (m-30) cc_final: 0.7861 (t0) REVERT: E 26 ASN cc_start: 0.7788 (t0) cc_final: 0.7490 (t0) REVERT: E 77 ASN cc_start: 0.7399 (t0) cc_final: 0.6867 (t0) REVERT: E 79 GLN cc_start: 0.6242 (mm-40) cc_final: 0.5810 (mm110) REVERT: F 70 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.7375 (mtp85) REVERT: F 82 ASP cc_start: 0.7476 (t0) cc_final: 0.6757 (m-30) REVERT: I 26 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7975 (mtp85) REVERT: I 72 ASP cc_start: 0.7361 (t0) cc_final: 0.6957 (t70) REVERT: I 82 ASN cc_start: 0.6735 (t0) cc_final: 0.6504 (t0) REVERT: K 50 THR cc_start: 0.8490 (t) cc_final: 0.8239 (t) REVERT: K 100 MET cc_start: 0.8560 (mtp) cc_final: 0.8306 (mtm) REVERT: K 102 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: K 186 ASN cc_start: 0.8160 (t0) cc_final: 0.7903 (t0) REVERT: K 397 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7889 (t0) REVERT: M 28 ASN cc_start: 0.7878 (p0) cc_final: 0.7273 (p0) REVERT: M 74 ASP cc_start: 0.8867 (m-30) cc_final: 0.8036 (p0) REVERT: N 3 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6673 (mm-40) REVERT: N 77 ASN cc_start: 0.7043 (t0) cc_final: 0.6718 (t0) REVERT: N 79 GLN cc_start: 0.6319 (mm110) cc_final: 0.5983 (mm110) REVERT: O 27 GLN cc_start: 0.7855 (tm-30) cc_final: 0.6890 (tm-30) REVERT: O 79 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: P 3 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6603 (t80) REVERT: P 26 ARG cc_start: 0.7272 (mtm110) cc_final: 0.7005 (mtp180) REVERT: P 66 ARG cc_start: 0.6367 (mtp180) cc_final: 0.5917 (ttp-110) outliers start: 46 outliers final: 32 residues processed: 325 average time/residue: 0.7307 time to fit residues: 273.6769 Evaluate side-chains 343 residues out of total 2763 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 84 SER Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 3 TYR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 397 ASN Chi-restraints excluded: chain M residue 18 VAL Chi-restraints excluded: chain M residue 84 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 21 ILE Chi-restraints excluded: chain O residue 29 ILE Chi-restraints excluded: chain O residue 79 GLN Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 TYR Chi-restraints excluded: chain P residue 89 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 239 optimal weight: 0.3980 chunk 279 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 293 optimal weight: 6.9990 chunk 222 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 146 ASN S 28 ASN H 96 HIS ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN D 6 GLN D 28 ASN K 146 ASN N 26 ASN P 96 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.114056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078328 restraints weight = 46666.973| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.15 r_work: 0.2952 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28345 Z= 0.122 Angle : 0.804 59.199 38909 Z= 0.399 Chirality : 0.045 0.347 4804 Planarity : 0.004 0.056 4598 Dihedral : 9.434 79.401 7325 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.31 % Rotamer: Outliers : 1.59 % Allowed : 15.64 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.16), residues: 3111 helix: 1.96 (0.29), residues: 342 sheet: 0.51 (0.16), residues: 1038 loop : -0.63 (0.16), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 103 TYR 0.016 0.001 TYR G 173 PHE 0.007 0.001 PHE K 383 TRP 0.019 0.001 TRP B 571 HIS 0.001 0.000 HIS J 564 Details of bonding type rmsd covalent geometry : bond 0.00270 (28103) covalent geometry : angle 0.78082 (38231) SS BOND : bond 0.00419 ( 48) SS BOND : angle 0.89297 ( 96) hydrogen bonds : bond 0.03521 ( 710) hydrogen bonds : angle 4.55880 ( 1827) link_ALPHA1-2 : bond 0.00376 ( 6) link_ALPHA1-2 : angle 1.68993 ( 18) link_ALPHA1-3 : bond 0.01140 ( 24) link_ALPHA1-3 : angle 2.60124 ( 72) link_ALPHA1-6 : bond 0.00726 ( 27) link_ALPHA1-6 : angle 1.70082 ( 81) link_BETA1-4 : bond 0.00446 ( 59) link_BETA1-4 : angle 1.36127 ( 177) link_BETA1-6 : bond 0.00578 ( 3) link_BETA1-6 : angle 1.07985 ( 9) link_NAG-ASN : bond 0.00174 ( 75) link_NAG-ASN : angle 1.72226 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9253.20 seconds wall clock time: 158 minutes 50.11 seconds (9530.11 seconds total)