Starting phenix.real_space_refine on Sun Aug 24 14:58:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fuu_3308/08_2025/5fuu_3308_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fuu_3308/08_2025/5fuu_3308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5fuu_3308/08_2025/5fuu_3308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fuu_3308/08_2025/5fuu_3308.map" model { file = "/net/cci-nas-00/data/ceres_data/5fuu_3308/08_2025/5fuu_3308_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fuu_3308/08_2025/5fuu_3308_neut.cif" } resolution = 4.19 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 12882 2.51 5 N 3274 2.21 5 O 4463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 20735 Number of models: 1 Model: "" Number of chains: 70 Chain: "A" Number of atoms: 3553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3553 Classifications: {'peptide': 449} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "B" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1150 Classifications: {'peptide': 144} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 141} Chain: "C" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3506 Classifications: {'peptide': 444} Link IDs: {'CIS': 3, 'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1159 Classifications: {'peptide': 147} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 142} Chain: "E" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3537 Classifications: {'peptide': 448} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1209 Classifications: {'peptide': 153} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 148} Chain: "H" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 127} Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "M" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1067 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "N" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" 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: "J" 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: "K" 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: 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: "P" 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: "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: 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: "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: 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: "V" 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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "Z" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 160 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 3, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "a" 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 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: "e" 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: "f" 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: "g" 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: "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: 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: "j" 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 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: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "y" Number of atoms: 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: "z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 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: "3" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "7" 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: "8" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} 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: "9" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 135 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "AA" 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: "BA" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 149 Unusual residues: {'BMA': 1, 'FUC': 1, 'GAL': 2, 'MAN': 2, 'NAG': 6} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 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: 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: 4.21, per 1000 atoms: 0.20 Number of scatterers: 20735 At special positions: 0 Unit cell: (137.55, 153.27, 140.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 4463 8.00 N 3274 7.00 C 12882 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.02 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 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 Atom "HETATM20028 O5 NAG 3 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM18843 O5 NAG a 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-2 " MAN 8 4 " - " MAN 8 5 " " MAN O 4 " - " MAN O 5 " " MAN f 4 " - " MAN f 5 " " MAN p 4 " - " MAN p 5 " " MAN x 4 " - " MAN x 5 " " MAN y 4 " - " MAN y 5 " ALPHA1-3 " BMA 8 3 " - " MAN 8 4 " " MAN 8 6 " - " MAN 8 7 " " BMA 9 3 " - " MAN 9 9 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA Y 3 " - " MAN Y 9 " " BMA Z 3 " - " MAN Z 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA p 3 " - " MAN p 4 " " MAN p 6 " - " MAN p 7 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " " MAN y 6 " - " MAN y 7 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA 6 3 " - " MAN 6 4 " " BMA 8 3 " - " MAN 8 6 " " MAN 8 6 " - " MAN 8 8 " " BMA 9 3 " - " MAN 9 4 " " BMA O 3 " - " MAN O 6 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 9 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 6 " " BMA p 3 " - " MAN p 6 " " MAN p 6 " - " MAN p 8 " " BMA x 3 " - " MAN x 6 " " BMA y 3 " - " MAN y 6 " " BMABA 3 " - " MANBA 9 " BETA1-2 " MAN 9 4 " - " NAG 9 5 " " MAN 9 9 " - " NAG 9 10 " " MAN Y 4 " - " NAG Y 5 " " MAN Y 9 " - " NAG Y 10 " " MAN Z 4 " - " NAG Z 5 " " MAN Z 9 " - " NAG Z 10 " " MANBA 4 " - " NAGBA 5 " " MANBA 9 " - " NAGBA 10 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG 9 5 " - " GAL 9 6 " " NAG 9 7 " - " GAL 9 8 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " 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 O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 S 2 " - " BMA S 3 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Y 5 " - " GAL Y 6 " " NAG Y 7 " - " GAL Y 8 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " MAN Z 4 " - " NAG Z 7 " " NAG Z 5 " - " GAL Z 6 " " NAG Z 7 " - " GAL Z 8 " " NAG Z 10 " - " GAL Z 11 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " 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 i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " 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 t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " 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 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " MANBA 4 " - " NAGBA 7 " " NAGBA 5 " - " GALBA 6 " " NAGBA 7 " - " GALBA 8 " BETA1-6 " NAG 9 1 " - " FUC 9 11 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " MAN 9 4 " - " NAG 9 7 " " NAG Y 1 " - " FUC Y 11 " " MAN Y 4 " - " NAG Y 7 " " NAG Z 1 " - " FUC Z 13 " " MAN Z 9 " - " NAG Z 12 " " NAG q 1 " - " FUC q 3 " " NAGBA 1 " - " FUCBA 12 " " MANBA 9 " - " NAGBA 11 " NAG-ASN " NAG 0 1 " - " ASN E 295 " " NAG 1 1 " - " ASN E 301 " " NAG 2 1 " - " ASN E 332 " " NAG 3 1 " - " ASN E 339 " " NAG 4 1 " - " ASN E 355 " " NAG 5 1 " - " ASN E 362 " " NAG 6 1 " - " ASN E 386 " " NAG 7 1 " - " ASN E 392 " " NAG 8 1 " - " ASN E 448 " " NAG 9 1 " - " ASN F 611 " " NAG A1135 " - " ASN A 135 " " NAG A1355 " - " ASN A 355 " " NAG A1397 " - " ASN A 397 " " NAG B1600 " - " ASN B 616 " " NAG B1625 " - " ASN B 625 " " NAG C1397 " - " ASN C 397 " " NAG D1600 " - " ASN D 616 " " NAG E1187 " - " ASN E 187 " " NAG E1397 " - " ASN E 397 " " NAG F1600 " - " ASN F 616 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 160 " " NAG K 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 276 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 301 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 339 " " NAG U 1 " - " ASN A 362 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 392 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN B 611 " " NAG Z 1 " - " ASN B 637 " " NAG a 1 " - " ASN C 88 " " NAG b 1 " - " ASN C 135 " " NAG c 1 " - " ASN C 156 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 241 " " NAG f 1 " - " ASN C 262 " " NAG g 1 " - " ASN C 276 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 339 " " NAG l 1 " - " ASN C 355 " " NAG m 1 " - " ASN C 362 " " NAG n 1 " - " ASN C 386 " " NAG o 1 " - " ASN C 392 " " NAG p 1 " - " ASN C 448 " " NAG q 1 " - " ASN D 611 " " NAG r 1 " - " ASN D 625 " " NAG s 1 " - " ASN D 637 " " NAG t 1 " - " ASN E 88 " " NAG u 1 " - " ASN E 135 " " NAG v 1 " - " ASN E 156 " " NAG w 1 " - " ASN E 160 " " NAG x 1 " - " ASN E 241 " " NAG y 1 " - " ASN E 262 " " NAG z 1 " - " ASN E 276 " " NAGAA 1 " - " ASN F 625 " " NAGBA 1 " - " ASN F 637 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 526.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4240 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 54 sheets defined 23.9% alpha, 39.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.887A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 529 through 541 removed outlier: 6.551A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 566 removed outlier: 4.110A pdb=" N ALA B 561 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.802A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 634 removed outlier: 3.581A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 651 removed outlier: 4.402A pdb=" N SER B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 663 removed outlier: 4.176A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.838A pdb=" N ILE C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.689A pdb=" N LYS C 348 " --> pdb=" O GLN C 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.677A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.649A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 555 through 564 removed outlier: 3.511A pdb=" N GLN D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 597 removed outlier: 3.852A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 657 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.230A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 353 removed outlier: 3.590A pdb=" N GLN E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.720A pdb=" N PHE E 391 " --> pdb=" O SER E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.624A pdb=" N GLU E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 464 removed outlier: 3.711A pdb=" N ASN E 463 " --> pdb=" O ILE E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 4.272A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.738A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 566 removed outlier: 3.662A pdb=" N ARG F 557 " --> pdb=" O ASN F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 removed outlier: 4.170A pdb=" N LEU F 592 " --> pdb=" O GLY F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.619A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 652 Processing helix chain 'F' and resid 655 through 662 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.726A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing sheet with id=AA, first strand: chain 'A' and resid 494 through 497 removed outlier: 4.216A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AD, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AE, first strand: chain 'A' and resid 171 through 177 removed outlier: 4.593A pdb=" N SER A 190 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AG, first strand: chain 'A' and resid 256 through 257 removed outlier: 4.052A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 381 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 383 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 12.992A pdb=" N PHE A 382 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 419 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.381A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'A' and resid 256 through 257 removed outlier: 4.052A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 381 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 383 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 12.992A pdb=" N PHE A 382 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 419 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.378A pdb=" N LEU A 260 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain 'A' and resid 256 through 257 removed outlier: 4.052A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 381 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE A 383 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 12.992A pdb=" N PHE A 382 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 419 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.381A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 260 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.792A pdb=" N ASN A 302 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE A 322 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG A 304 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLY A 321 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER A 306 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR A 319 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N HIS A 308 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N PHE A 317 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id=CA, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.141A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.080A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=CD, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=CE, first strand: chain 'C' and resid 129 through 130 removed outlier: 3.741A pdb=" N ARG C 192 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing sheet with id=CF, first strand: chain 'C' and resid 155 through 157 Processing sheet with id=CG, first strand: chain 'C' and resid 202 through 203 Processing sheet with id=CH, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.982A pdb=" N LEU C 260 " --> pdb=" O ASN C 448 " (cutoff:3.500A) Processing sheet with id=CI, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=CJ, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.335A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 11.293A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.859A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.975A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.742A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS C 445 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=CK, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.335A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=CL, first strand: chain 'C' and resid 301 through 308 removed outlier: 7.193A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=DA, first strand: chain 'D' and resid 513 through 515 Processing sheet with id=EA, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.181A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.934A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=ED, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=EE, first strand: chain 'E' and resid 120 through 121 removed outlier: 3.972A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) Processing sheet with id=EF, first strand: chain 'E' and resid 129 through 130 Processing sheet with id=EG, first strand: chain 'E' and resid 154 through 162 Processing sheet with id=EH, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.927A pdb=" N LEU E 260 " --> pdb=" O ASN E 448 " (cutoff:3.500A) Processing sheet with id=EI, first strand: chain 'E' and resid 271 through 274 Processing sheet with id=EJ, first strand: chain 'E' and resid 374 through 377 removed outlier: 6.074A pdb=" N PHE E 383 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N CYS E 385 " --> pdb=" O PHE E 376 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS E 331 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE E 333 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 13.518A pdb=" N CYS E 418 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 13.624A pdb=" N HIS E 330 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN E 295 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR E 297 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.812A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.018A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.915A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.846A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing sheet with id=EK, first strand: chain 'E' and resid 374 through 377 removed outlier: 6.074A pdb=" N PHE E 383 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N CYS E 385 " --> pdb=" O PHE E 376 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N CYS E 331 " --> pdb=" O ILE E 414 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE E 333 " --> pdb=" O LEU E 416 " (cutoff:3.500A) removed outlier: 13.518A pdb=" N CYS E 418 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 13.624A pdb=" N HIS E 330 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASN E 295 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR E 297 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing sheet with id=EL, first strand: chain 'E' and resid 302 through 312 removed outlier: 6.755A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=FA, first strand: chain 'F' and resid 513 through 515 Processing sheet with id=HA, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=HB, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.158A pdb=" N THR H 108 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=HC, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.158A pdb=" N THR H 108 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=HD, first strand: chain 'H' and resid 100R through 103 removed outlier: 6.940A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) Processing sheet with id=LA, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.599A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=LB, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.694A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=LC, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.872A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN L 53 " --> pdb=" O PHE L 49 " (cutoff:3.500A) Processing sheet with id=LD, first strand: chain 'L' and resid 97 through 98 removed outlier: 3.694A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=MA, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=MB, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.076A pdb=" N THR M 108 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=MC, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.076A pdb=" N THR M 108 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N MET M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=MD, first strand: chain 'M' and resid 100R through 103 removed outlier: 6.661A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) Processing sheet with id=NA, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=NB, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=NC, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.142A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=ND, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=NE, first strand: chain 'N' and resid 27C through 27D removed outlier: 3.678A pdb=" N LYS N 30 " --> pdb=" O GLN N 27D" (cutoff:3.500A) 775 hydrogen bonds defined for protein. 2016 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: 3.88 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4977 1.33 - 1.45: 5227 1.45 - 1.57: 10733 1.57 - 1.69: 0 1.69 - 1.81: 164 Bond restraints: 21101 Sorted by residual: bond pdb=" CA ASN A 229 " pdb=" CB ASN A 229 " ideal model delta sigma weight residual 1.530 1.412 0.117 1.64e-02 3.72e+03 5.11e+01 bond pdb=" N PRO E 118 " pdb=" CD PRO E 118 " ideal model delta sigma weight residual 1.473 1.553 -0.080 1.40e-02 5.10e+03 3.25e+01 bond pdb=" N PRO A 118 " pdb=" CD PRO A 118 " ideal model delta sigma weight residual 1.473 1.549 -0.076 1.40e-02 5.10e+03 2.91e+01 bond pdb=" CA SER F 599 " pdb=" C SER F 599 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.28e-02 6.10e+03 2.58e+01 bond pdb=" C ASN E 80 " pdb=" N PRO E 81 " ideal model delta sigma weight residual 1.334 1.389 -0.055 1.11e-02 8.12e+03 2.45e+01 ... (remaining 21096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 25249 2.61 - 5.21: 2560 5.21 - 7.82: 625 7.82 - 10.43: 169 10.43 - 13.03: 27 Bond angle restraints: 28630 Sorted by residual: angle pdb=" C GLY M 100 " pdb=" N PRO M 100A" pdb=" CA PRO M 100A" ideal model delta sigma weight residual 119.66 128.29 -8.63 7.30e-01 1.88e+00 1.40e+02 angle pdb=" C ASN C 80 " pdb=" N PRO C 81 " pdb=" CA PRO C 81 " ideal model delta sigma weight residual 119.99 130.47 -10.48 1.08e+00 8.57e-01 9.42e+01 angle pdb=" C GLY C 237 " pdb=" N PRO C 238 " pdb=" CA PRO C 238 " ideal model delta sigma weight residual 119.76 128.86 -9.10 1.00e+00 1.00e+00 8.29e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.32 129.28 -9.96 1.14e+00 7.69e-01 7.64e+01 angle pdb=" C ALA C 436 " pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 119.66 125.92 -6.26 7.20e-01 1.93e+00 7.57e+01 ... (remaining 28625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.70: 14752 26.70 - 53.39: 271 53.39 - 80.09: 230 80.09 - 106.78: 135 106.78 - 133.48: 4 Dihedral angle restraints: 15392 sinusoidal: 8822 harmonic: 6570 Sorted by residual: dihedral pdb=" CA ASN E 412 " pdb=" C ASN E 412 " pdb=" N THR E 413 " pdb=" CA THR E 413 " ideal model delta harmonic sigma weight residual -180.00 -46.52 -133.48 0 5.00e+00 4.00e-02 7.13e+02 dihedral pdb=" CA VAL C 65 " pdb=" C VAL C 65 " pdb=" N HIS C 66 " pdb=" CA HIS C 66 " ideal model delta harmonic sigma weight residual 0.00 -37.56 37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" C GLN C 352 " pdb=" N GLN C 352 " pdb=" CA GLN C 352 " pdb=" CB GLN C 352 " ideal model delta harmonic sigma weight residual -122.60 -140.88 18.28 0 2.50e+00 1.60e-01 5.35e+01 ... (remaining 15389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 3170 0.158 - 0.317: 638 0.317 - 0.475: 19 0.475 - 0.634: 13 0.634 - 0.792: 10 Chirality restraints: 3850 Sorted by residual: chirality pdb=" C1 MAN f 7 " pdb=" O3 MAN f 6 " pdb=" C2 MAN f 7 " pdb=" O5 MAN f 7 " both_signs ideal model delta sigma weight residual False 2.40 1.62 0.78 2.00e-02 2.50e+03 1.51e+03 chirality pdb=" C1 MAN O 7 " pdb=" O3 MAN O 6 " pdb=" C2 MAN O 7 " pdb=" O5 MAN O 7 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.50e+03 chirality pdb=" C1 MAN y 7 " pdb=" O3 MAN y 6 " pdb=" C2 MAN y 7 " pdb=" O5 MAN y 7 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.50e+03 ... (remaining 3847 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 301 " -0.300 2.00e-02 2.50e+03 3.39e-01 1.44e+03 pdb=" CG ASN C 301 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN C 301 " 0.094 2.00e-02 2.50e+03 pdb=" ND2 ASN C 301 " 0.505 2.00e-02 2.50e+03 pdb=" C1 NAG i 1 " -0.446 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 156 " 0.258 2.00e-02 2.50e+03 3.37e-01 1.42e+03 pdb=" CG ASN A 156 " -0.143 2.00e-02 2.50e+03 pdb=" OD1 ASN A 156 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 156 " -0.526 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.450 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.308 2.00e-02 2.50e+03 3.32e-01 1.38e+03 pdb=" CG ASN C 156 " 0.146 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " 0.128 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " 0.474 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " -0.440 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 173 2.48 - 3.08: 15649 3.08 - 3.69: 28449 3.69 - 4.29: 44804 4.29 - 4.90: 70198 Nonbonded interactions: 159273 Sorted by model distance: nonbonded pdb=" CA PRO E 183 " pdb=" CD1 TYR E 191 " model vdw 1.869 3.770 nonbonded pdb=" OD1 ASN A 339 " pdb=" N ASP A 340 " model vdw 1.900 3.120 nonbonded pdb=" O ALA E 336 " pdb=" OD1 ASN E 339 " model vdw 1.967 3.040 nonbonded pdb=" OE1 GLU A 87 " pdb=" O7 NAG G 1 " model vdw 1.996 3.040 nonbonded pdb=" O3 GAL Y 6 " pdb=" O2 MAN x 6 " model vdw 2.000 3.040 ... (remaining 159268 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 '1' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain 'AA' selection = chain 'G' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'r' selection = chain 's' selection = chain 'u' selection = chain 'w' selection = chain 'z' } ncs_group { reference = (chain '2' and resid 1 through 2) selection = (chain '7' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'v' and resid 1 through 2) } ncs_group { reference = (chain '8' and (resid 2 or resid 5 through 8)) selection = (chain 'O' and (resid 1 or resid 4 through 7)) selection = (chain 'f' and (resid 1 or resid 4 through 7)) selection = (chain 'p' and (resid 2 or resid 5 through 8)) selection = (chain 'y' and (resid 1 or resid 4 through 7)) } ncs_group { reference = (chain '9' and (resid 1 or resid 10 through 11)) selection = (chain 'BA' and (resid 2 or resid 11 through 12)) selection = (chain 'Y' and (resid 1 or resid 10 through 11)) } ncs_group { reference = (chain 'A' and (resid 31 through 136 or resid 152 through 401 or resid 410 throu \ gh 506 or resid 1397)) selection = (chain 'C' and (resid 31 through 57 or resid 64 through 401 or resid 410 through \ 1397)) selection = (chain 'E' and (resid 31 through 57 or resid 64 through 136 or resid 152 through \ 401 or resid 410 through 506 or resid 1397)) } ncs_group { reference = (chain 'B' and resid 521 through 658) selection = (chain 'D' and resid 521 through 658) selection = (chain 'F' and resid 521 through 658) } ncs_group { reference = (chain 'H' and resid 2 through 113) selection = (chain 'M' and resid 2 through 113) } ncs_group { reference = (chain 'L' and resid 2 through 108) selection = chain 'N' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.450 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 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 : 0.015 0.432 21349 Z= 0.942 Angle : 2.291 44.759 29337 Z= 1.150 Chirality : 0.120 0.792 3850 Planarity : 0.017 0.137 3338 Dihedral : 17.626 133.475 11050 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 1.69 % Allowed : 6.15 % Favored : 92.15 % Rotamer: Outliers : 1.20 % Allowed : 1.54 % Favored : 97.26 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.15), residues: 2243 helix: -1.70 (0.20), residues: 431 sheet: -1.02 (0.20), residues: 600 loop : -1.82 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.003 ARG C 503 TYR 0.003 0.000 TYR M 100N PHE 0.010 0.000 PHE B 522 TRP 0.001 0.000 TRP M 100G HIS 0.003 0.000 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.01402 (21101) covalent geometry : angle 1.86196 (28630) SS BOND : bond 0.00679 ( 34) SS BOND : angle 10.55215 ( 68) hydrogen bonds : bond 0.17019 ( 688) hydrogen bonds : angle 8.33279 ( 2016) Misc. bond : bond 0.43203 ( 1) link_ALPHA1-2 : bond 0.02252 ( 6) link_ALPHA1-2 : angle 3.06926 ( 18) link_ALPHA1-3 : bond 0.03391 ( 16) link_ALPHA1-3 : angle 5.13624 ( 48) link_ALPHA1-6 : bond 0.04268 ( 14) link_ALPHA1-6 : angle 5.20510 ( 42) link_BETA1-2 : bond 0.03276 ( 8) link_BETA1-2 : angle 3.54094 ( 24) link_BETA1-4 : bond 0.04159 ( 96) link_BETA1-4 : angle 5.50298 ( 288) link_BETA1-6 : bond 0.03395 ( 9) link_BETA1-6 : angle 3.45882 ( 27) link_NAG-ASN : bond 0.03983 ( 64) link_NAG-ASN : angle 13.55689 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 562 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.8288 (m-90) cc_final: 0.7344 (m-10) REVERT: A 217 TYR cc_start: 0.8219 (m-80) cc_final: 0.7468 (m-10) REVERT: A 229 ASN cc_start: 0.6352 (m110) cc_final: 0.5984 (m110) REVERT: A 434 MET cc_start: 0.8581 (tmm) cc_final: 0.8275 (ttm) REVERT: A 499 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6464 (t) REVERT: B 543 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 554 ASN cc_start: 0.7501 (m-40) cc_final: 0.7024 (t0) REVERT: B 606 THR cc_start: 0.8556 (t) cc_final: 0.8326 (p) REVERT: B 628 TRP cc_start: 0.8507 (t-100) cc_final: 0.8268 (t-100) REVERT: B 663 LEU cc_start: 0.7516 (mt) cc_final: 0.7288 (mt) REVERT: C 100 MET cc_start: 0.7585 (mtp) cc_final: 0.7271 (mtm) REVERT: C 297 THR cc_start: 0.7138 (p) cc_final: 0.6850 (p) REVERT: C 434 MET cc_start: 0.8329 (ppp) cc_final: 0.8114 (ptp) REVERT: C 482 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7439 (mm-30) REVERT: D 584 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7329 (mt-10) REVERT: D 646 ILE cc_start: 0.9388 (mt) cc_final: 0.9173 (mt) REVERT: E 42 VAL cc_start: 0.9667 (t) cc_final: 0.9448 (p) REVERT: E 45 TRP cc_start: 0.7838 (m-10) cc_final: 0.7633 (m-10) REVERT: E 56 SER cc_start: 0.9043 (p) cc_final: 0.8795 (m) REVERT: E 57 ASP cc_start: 0.7473 (t0) cc_final: 0.7103 (t70) REVERT: E 213 ILE cc_start: 0.9177 (mt) cc_final: 0.8920 (tt) REVERT: F 629 MET cc_start: 0.7662 (mtm) cc_final: 0.6205 (mtm) REVERT: F 630 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7105 (mt-10) REVERT: H 22 CYS cc_start: 0.3418 (t) cc_final: 0.2734 (t) REVERT: M 72 ASP cc_start: 0.4572 (t0) cc_final: 0.3896 (t0) REVERT: M 82 MET cc_start: 0.6699 (mtm) cc_final: 0.6447 (mtp) outliers start: 24 outliers final: 11 residues processed: 583 average time/residue: 0.1443 time to fit residues: 122.3843 Evaluate side-chains 248 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 235 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS C 99 ASN C 389 GLN D 624 ASN E 66 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN F 624 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 76 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.083578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065550 restraints weight = 65215.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.067366 restraints weight = 39605.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.068564 restraints weight = 28804.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.069365 restraints weight = 23699.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069838 restraints weight = 20812.617| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21349 Z= 0.196 Angle : 1.122 19.017 29337 Z= 0.491 Chirality : 0.058 0.862 3850 Planarity : 0.005 0.046 3338 Dihedral : 15.398 84.109 6745 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.71 % Allowed : 4.32 % Favored : 94.96 % Rotamer: Outliers : 0.30 % Allowed : 2.19 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.16), residues: 2243 helix: -0.49 (0.23), residues: 442 sheet: -0.65 (0.20), residues: 582 loop : -1.39 (0.16), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 542 TYR 0.021 0.002 TYR E 191 PHE 0.020 0.002 PHE C 53 TRP 0.028 0.002 TRP E 479 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00397 (21101) covalent geometry : angle 0.99253 (28630) SS BOND : bond 0.00760 ( 34) SS BOND : angle 1.58397 ( 68) hydrogen bonds : bond 0.05681 ( 688) hydrogen bonds : angle 6.38466 ( 2016) Misc. bond : bond 0.01460 ( 1) link_ALPHA1-2 : bond 0.00735 ( 6) link_ALPHA1-2 : angle 1.48870 ( 18) link_ALPHA1-3 : bond 0.01448 ( 16) link_ALPHA1-3 : angle 2.01623 ( 48) link_ALPHA1-6 : bond 0.00808 ( 14) link_ALPHA1-6 : angle 1.94728 ( 42) link_BETA1-2 : bond 0.00592 ( 8) link_BETA1-2 : angle 1.89214 ( 24) link_BETA1-4 : bond 0.00694 ( 96) link_BETA1-4 : angle 2.89782 ( 288) link_BETA1-6 : bond 0.00521 ( 9) link_BETA1-6 : angle 1.78414 ( 27) link_NAG-ASN : bond 0.00785 ( 64) link_NAG-ASN : angle 5.37605 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 369 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8580 (t0) cc_final: 0.8197 (t0) REVERT: A 96 TRP cc_start: 0.8339 (m-90) cc_final: 0.7486 (m-10) REVERT: A 373 MET cc_start: 0.7731 (mmp) cc_final: 0.7342 (mmp) REVERT: A 426 MET cc_start: 0.8751 (tpt) cc_final: 0.8030 (tpp) REVERT: A 499 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7482 (t) REVERT: B 554 ASN cc_start: 0.7916 (m-40) cc_final: 0.7704 (t0) REVERT: B 628 TRP cc_start: 0.8623 (t-100) cc_final: 0.8340 (t-100) REVERT: B 655 LYS cc_start: 0.9188 (mmmt) cc_final: 0.8945 (mmmm) REVERT: C 34 LEU cc_start: 0.9074 (mt) cc_final: 0.8698 (mp) REVERT: C 297 THR cc_start: 0.8128 (p) cc_final: 0.7863 (p) REVERT: C 482 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8347 (mm-30) REVERT: D 530 MET cc_start: 0.7755 (mtm) cc_final: 0.7190 (mpp) REVERT: D 626 MET cc_start: 0.8747 (tpp) cc_final: 0.7914 (tpp) REVERT: D 629 MET cc_start: 0.7260 (tpp) cc_final: 0.6967 (tpp) REVERT: D 651 ASN cc_start: 0.8782 (m110) cc_final: 0.8547 (m-40) REVERT: E 42 VAL cc_start: 0.9450 (t) cc_final: 0.9224 (p) REVERT: E 45 TRP cc_start: 0.8193 (m-10) cc_final: 0.7989 (m-10) REVERT: E 318 TYR cc_start: 0.8123 (m-80) cc_final: 0.7837 (m-80) REVERT: E 484 TYR cc_start: 0.8983 (p90) cc_final: 0.8691 (p90) REVERT: E 486 TYR cc_start: 0.9117 (m-80) cc_final: 0.8782 (m-10) REVERT: F 520 LEU cc_start: 0.8412 (tp) cc_final: 0.8069 (tp) REVERT: F 629 MET cc_start: 0.8240 (mtm) cc_final: 0.5935 (mtm) REVERT: F 655 LYS cc_start: 0.8732 (tppt) cc_final: 0.8471 (mmtp) REVERT: F 658 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8453 (tm-30) REVERT: H 31 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8353 (mtpt) REVERT: H 45 LEU cc_start: 0.9238 (mt) cc_final: 0.8892 (mt) REVERT: H 98 GLU cc_start: 0.7695 (tt0) cc_final: 0.7200 (tt0) REVERT: H 100 ASP cc_start: 0.9251 (t0) cc_final: 0.8890 (t0) REVERT: L 47 LEU cc_start: 0.9286 (mm) cc_final: 0.9076 (mm) REVERT: L 73 LEU cc_start: 0.8792 (tp) cc_final: 0.8509 (tp) REVERT: M 95 MET cc_start: 0.8501 (ttm) cc_final: 0.8142 (ttm) REVERT: M 100 MET cc_start: 0.8778 (mpp) cc_final: 0.8572 (mpp) REVERT: N 27 GLU cc_start: 0.8488 (tp30) cc_final: 0.7977 (tp30) outliers start: 6 outliers final: 1 residues processed: 371 average time/residue: 0.1195 time to fit residues: 69.3412 Evaluate side-chains 227 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 225 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 175 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 136 optimal weight: 0.0030 chunk 77 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 2.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 246 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 553 ASN E 249 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN M 97 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.080975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.062322 restraints weight = 67849.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.064134 restraints weight = 41088.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.065343 restraints weight = 29902.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.066129 restraints weight = 24531.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066567 restraints weight = 21650.645| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21349 Z= 0.203 Angle : 1.015 30.099 29337 Z= 0.442 Chirality : 0.054 0.500 3850 Planarity : 0.004 0.040 3338 Dihedral : 12.372 76.897 6745 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.67 % Allowed : 5.13 % Favored : 94.20 % Rotamer: Outliers : 0.20 % Allowed : 2.09 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.78 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.17), residues: 2243 helix: -0.27 (0.24), residues: 446 sheet: -0.54 (0.20), residues: 612 loop : -1.24 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 298 TYR 0.015 0.002 TYR D 638 PHE 0.018 0.002 PHE E 53 TRP 0.027 0.002 TRP L 35 HIS 0.007 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00437 (21101) covalent geometry : angle 0.91667 (28630) SS BOND : bond 0.00586 ( 34) SS BOND : angle 1.78042 ( 68) hydrogen bonds : bond 0.05047 ( 688) hydrogen bonds : angle 5.94907 ( 2016) Misc. bond : bond 0.01027 ( 1) link_ALPHA1-2 : bond 0.00715 ( 6) link_ALPHA1-2 : angle 1.61277 ( 18) link_ALPHA1-3 : bond 0.01130 ( 16) link_ALPHA1-3 : angle 1.60568 ( 48) link_ALPHA1-6 : bond 0.00750 ( 14) link_ALPHA1-6 : angle 2.09161 ( 42) link_BETA1-2 : bond 0.00617 ( 8) link_BETA1-2 : angle 1.79883 ( 24) link_BETA1-4 : bond 0.00429 ( 96) link_BETA1-4 : angle 2.59486 ( 288) link_BETA1-6 : bond 0.00492 ( 9) link_BETA1-6 : angle 1.76090 ( 27) link_NAG-ASN : bond 0.00550 ( 64) link_NAG-ASN : angle 4.24913 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 314 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8604 (t0) cc_final: 0.8375 (t0) REVERT: B 554 ASN cc_start: 0.7808 (m-40) cc_final: 0.6374 (t0) REVERT: B 565 MET cc_start: 0.6992 (mtt) cc_final: 0.6727 (tmm) REVERT: B 629 MET cc_start: 0.8513 (tpp) cc_final: 0.7954 (tpp) REVERT: B 655 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8994 (mmmm) REVERT: C 34 LEU cc_start: 0.9043 (mt) cc_final: 0.8753 (mp) REVERT: C 100 MET cc_start: 0.8660 (mtm) cc_final: 0.8376 (mtm) REVERT: C 297 THR cc_start: 0.7922 (p) cc_final: 0.7643 (p) REVERT: C 373 MET cc_start: 0.8754 (mmm) cc_final: 0.8331 (mmm) REVERT: C 482 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8482 (mm-30) REVERT: D 530 MET cc_start: 0.7701 (mtm) cc_final: 0.7105 (mpp) REVERT: D 603 ILE cc_start: 0.9466 (mt) cc_final: 0.9165 (mt) REVERT: D 626 MET cc_start: 0.8935 (tpp) cc_final: 0.7579 (tpt) REVERT: D 636 ASP cc_start: 0.8891 (t70) cc_final: 0.8690 (t0) REVERT: D 641 GLU cc_start: 0.8471 (mp0) cc_final: 0.8225 (mp0) REVERT: D 647 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7684 (mp0) REVERT: E 318 TYR cc_start: 0.8069 (m-80) cc_final: 0.7775 (m-80) REVERT: E 484 TYR cc_start: 0.8978 (p90) cc_final: 0.8646 (p90) REVERT: E 486 TYR cc_start: 0.9157 (m-80) cc_final: 0.8773 (m-80) REVERT: E 505 VAL cc_start: 0.8416 (p) cc_final: 0.8116 (p) REVERT: F 642 ILE cc_start: 0.9569 (mt) cc_final: 0.9348 (mm) REVERT: F 658 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8574 (tm-30) REVERT: H 31 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8357 (mtpt) REVERT: H 45 LEU cc_start: 0.9036 (mt) cc_final: 0.8784 (mt) REVERT: H 72 ASP cc_start: 0.7890 (t0) cc_final: 0.7682 (t0) REVERT: H 98 GLU cc_start: 0.7588 (tt0) cc_final: 0.7013 (tt0) REVERT: H 100 ASP cc_start: 0.9463 (t0) cc_final: 0.9202 (t0) REVERT: L 27 ARG cc_start: 0.8262 (tpp80) cc_final: 0.7705 (tpp80) REVERT: L 34 TYR cc_start: 0.8949 (m-80) cc_final: 0.8711 (m-80) REVERT: L 36 TYR cc_start: 0.7989 (m-80) cc_final: 0.6936 (m-80) REVERT: L 46 LEU cc_start: 0.8799 (tt) cc_final: 0.8339 (tp) REVERT: L 73 LEU cc_start: 0.8710 (tp) cc_final: 0.7886 (tp) REVERT: L 77 ARG cc_start: 0.8093 (mpp80) cc_final: 0.7866 (mpp80) REVERT: M 82 MET cc_start: 0.8423 (mtp) cc_final: 0.8194 (mtm) REVERT: M 97 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6419 (tm-30) REVERT: M 98 GLU cc_start: 0.6992 (pt0) cc_final: 0.6775 (pt0) REVERT: N 27 GLU cc_start: 0.8670 (tp30) cc_final: 0.8099 (tp30) outliers start: 4 outliers final: 1 residues processed: 317 average time/residue: 0.1166 time to fit residues: 57.7639 Evaluate side-chains 224 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 42 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 551 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN H 39 GLN N 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.078497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.060725 restraints weight = 68625.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.062354 restraints weight = 42391.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.062951 restraints weight = 30335.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.063271 restraints weight = 27145.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063450 restraints weight = 25711.262| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21349 Z= 0.269 Angle : 1.011 27.730 29337 Z= 0.447 Chirality : 0.054 0.477 3850 Planarity : 0.005 0.049 3338 Dihedral : 10.964 70.576 6745 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.42 % Favored : 93.13 % Rotamer: Outliers : 0.10 % Allowed : 2.34 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.17), residues: 2243 helix: -0.05 (0.25), residues: 433 sheet: -0.58 (0.20), residues: 600 loop : -1.27 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 557 TYR 0.019 0.002 TYR D 638 PHE 0.019 0.002 PHE E 53 TRP 0.043 0.003 TRP L 35 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00591 (21101) covalent geometry : angle 0.92421 (28630) SS BOND : bond 0.00461 ( 34) SS BOND : angle 1.82682 ( 68) hydrogen bonds : bond 0.04985 ( 688) hydrogen bonds : angle 5.89652 ( 2016) Misc. bond : bond 0.00605 ( 1) link_ALPHA1-2 : bond 0.00684 ( 6) link_ALPHA1-2 : angle 1.57092 ( 18) link_ALPHA1-3 : bond 0.01109 ( 16) link_ALPHA1-3 : angle 1.80915 ( 48) link_ALPHA1-6 : bond 0.00728 ( 14) link_ALPHA1-6 : angle 2.03353 ( 42) link_BETA1-2 : bond 0.00614 ( 8) link_BETA1-2 : angle 2.03379 ( 24) link_BETA1-4 : bond 0.00398 ( 96) link_BETA1-4 : angle 2.48830 ( 288) link_BETA1-6 : bond 0.00530 ( 9) link_BETA1-6 : angle 1.97409 ( 27) link_NAG-ASN : bond 0.00584 ( 64) link_NAG-ASN : angle 3.92217 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ASN cc_start: 0.8773 (t0) cc_final: 0.8555 (t0) REVERT: A 95 MET cc_start: 0.8707 (ppp) cc_final: 0.8270 (ppp) REVERT: A 104 MET cc_start: 0.8945 (tpp) cc_final: 0.8441 (tpp) REVERT: A 217 TYR cc_start: 0.8290 (m-80) cc_final: 0.7422 (m-10) REVERT: B 565 MET cc_start: 0.7153 (mtt) cc_final: 0.6714 (tmm) REVERT: B 629 MET cc_start: 0.8423 (tpp) cc_final: 0.7932 (tpp) REVERT: C 34 LEU cc_start: 0.9062 (mt) cc_final: 0.8772 (mp) REVERT: C 95 MET cc_start: 0.8735 (ptm) cc_final: 0.8527 (ptm) REVERT: C 100 MET cc_start: 0.8778 (mtm) cc_final: 0.8421 (mtm) REVERT: C 482 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8615 (mm-30) REVERT: D 641 GLU cc_start: 0.8507 (mp0) cc_final: 0.8258 (mp0) REVERT: D 647 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7759 (mp0) REVERT: E 184 ILE cc_start: 0.8148 (mt) cc_final: 0.7931 (mm) REVERT: E 318 TYR cc_start: 0.8291 (m-80) cc_final: 0.7999 (m-80) REVERT: E 484 TYR cc_start: 0.8913 (p90) cc_final: 0.8498 (p90) REVERT: E 505 VAL cc_start: 0.8342 (p) cc_final: 0.8110 (p) REVERT: F 535 MET cc_start: 0.8066 (mpp) cc_final: 0.7810 (mpp) REVERT: F 595 ILE cc_start: 0.9442 (mt) cc_final: 0.9224 (mm) REVERT: H 31 LYS cc_start: 0.8765 (mtpt) cc_final: 0.8384 (mtpt) REVERT: H 86 ASP cc_start: 0.8268 (m-30) cc_final: 0.7999 (m-30) REVERT: H 98 GLU cc_start: 0.7702 (tt0) cc_final: 0.7278 (tt0) REVERT: H 100 MET cc_start: 0.7903 (pmm) cc_final: 0.7607 (pmm) REVERT: L 13 VAL cc_start: 0.8046 (p) cc_final: 0.7735 (p) REVERT: L 14 THR cc_start: 0.7753 (p) cc_final: 0.7520 (p) REVERT: L 36 TYR cc_start: 0.8086 (m-80) cc_final: 0.6635 (m-80) REVERT: L 73 LEU cc_start: 0.8716 (tp) cc_final: 0.8188 (tp) REVERT: L 77 ARG cc_start: 0.8102 (mpp80) cc_final: 0.7882 (mpp80) REVERT: M 100 MET cc_start: 0.9150 (mpp) cc_final: 0.8782 (mpp) REVERT: N 27 GLU cc_start: 0.8638 (tp30) cc_final: 0.8146 (tp30) outliers start: 2 outliers final: 1 residues processed: 285 average time/residue: 0.1143 time to fit residues: 51.4368 Evaluate side-chains 205 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 59 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 214 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 51 optimal weight: 0.0870 chunk 120 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.080916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.062524 restraints weight = 67417.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.064323 restraints weight = 40338.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065559 restraints weight = 29274.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.066343 restraints weight = 23871.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.066782 restraints weight = 21011.694| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21349 Z= 0.145 Angle : 0.890 27.987 29337 Z= 0.394 Chirality : 0.051 0.452 3850 Planarity : 0.004 0.045 3338 Dihedral : 9.934 66.266 6745 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.57 % Favored : 94.07 % Rotamer: Outliers : 0.05 % Allowed : 1.54 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 2243 helix: 0.09 (0.25), residues: 436 sheet: -0.31 (0.21), residues: 587 loop : -1.25 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 94 TYR 0.016 0.001 TYR E 486 PHE 0.029 0.002 PHE H 29 TRP 0.056 0.002 TRP L 35 HIS 0.007 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00298 (21101) covalent geometry : angle 0.81296 (28630) SS BOND : bond 0.00454 ( 34) SS BOND : angle 1.59204 ( 68) hydrogen bonds : bond 0.04283 ( 688) hydrogen bonds : angle 5.62365 ( 2016) Misc. bond : bond 0.00307 ( 1) link_ALPHA1-2 : bond 0.00768 ( 6) link_ALPHA1-2 : angle 1.73657 ( 18) link_ALPHA1-3 : bond 0.01077 ( 16) link_ALPHA1-3 : angle 1.62489 ( 48) link_ALPHA1-6 : bond 0.00907 ( 14) link_ALPHA1-6 : angle 1.88490 ( 42) link_BETA1-2 : bond 0.00293 ( 8) link_BETA1-2 : angle 1.73047 ( 24) link_BETA1-4 : bond 0.00445 ( 96) link_BETA1-4 : angle 2.20682 ( 288) link_BETA1-6 : bond 0.00509 ( 9) link_BETA1-6 : angle 1.25902 ( 27) link_NAG-ASN : bond 0.00408 ( 64) link_NAG-ASN : angle 3.46027 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8693 (ppp) cc_final: 0.8422 (ppp) REVERT: A 104 MET cc_start: 0.8906 (tpp) cc_final: 0.8627 (tpp) REVERT: A 217 TYR cc_start: 0.8143 (m-80) cc_final: 0.7538 (m-80) REVERT: A 425 ASN cc_start: 0.8354 (t0) cc_final: 0.8067 (t0) REVERT: A 484 TYR cc_start: 0.8755 (p90) cc_final: 0.8549 (p90) REVERT: B 565 MET cc_start: 0.6956 (mtt) cc_final: 0.6693 (tmm) REVERT: B 651 ASN cc_start: 0.8082 (m110) cc_final: 0.7811 (m110) REVERT: C 100 MET cc_start: 0.8716 (mtm) cc_final: 0.8357 (mtm) REVERT: C 297 THR cc_start: 0.8130 (p) cc_final: 0.7841 (p) REVERT: C 373 MET cc_start: 0.8783 (mmm) cc_final: 0.8544 (mmp) REVERT: C 482 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8437 (mm-30) REVERT: D 530 MET cc_start: 0.7741 (mtp) cc_final: 0.7017 (ttm) REVERT: D 647 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7581 (mp0) REVERT: E 104 MET cc_start: 0.9135 (ttt) cc_final: 0.8928 (ttt) REVERT: E 318 TYR cc_start: 0.8264 (m-80) cc_final: 0.7883 (m-80) REVERT: E 484 TYR cc_start: 0.8885 (p90) cc_final: 0.8414 (p90) REVERT: F 535 MET cc_start: 0.7919 (mpp) cc_final: 0.7487 (mpp) REVERT: F 629 MET cc_start: 0.7948 (mtt) cc_final: 0.6780 (mtt) REVERT: H 45 LEU cc_start: 0.8874 (mt) cc_final: 0.8551 (mt) REVERT: H 72 ASP cc_start: 0.7959 (t70) cc_final: 0.7645 (t0) REVERT: H 100 MET cc_start: 0.7904 (pmm) cc_final: 0.7616 (pmm) REVERT: L 58 VAL cc_start: 0.8116 (t) cc_final: 0.7903 (t) REVERT: L 82 ASP cc_start: 0.7561 (m-30) cc_final: 0.7315 (m-30) REVERT: M 95 MET cc_start: 0.8476 (ttm) cc_final: 0.7487 (ttp) REVERT: M 100 MET cc_start: 0.9122 (mpp) cc_final: 0.8656 (mpp) REVERT: N 27 GLU cc_start: 0.8648 (tp30) cc_final: 0.8196 (tp30) REVERT: N 45 GLN cc_start: 0.8365 (mm110) cc_final: 0.7618 (mm110) outliers start: 1 outliers final: 1 residues processed: 308 average time/residue: 0.1219 time to fit residues: 58.5926 Evaluate side-chains 204 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 88 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 168 optimal weight: 0.5980 chunk 127 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 206 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.080890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.062438 restraints weight = 67576.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064253 restraints weight = 40618.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065483 restraints weight = 29515.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.066248 restraints weight = 24099.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066766 restraints weight = 21319.028| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21349 Z= 0.143 Angle : 0.871 26.097 29337 Z= 0.388 Chirality : 0.050 0.453 3850 Planarity : 0.004 0.038 3338 Dihedral : 9.364 63.089 6745 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.66 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.17), residues: 2243 helix: 0.22 (0.25), residues: 436 sheet: -0.40 (0.20), residues: 625 loop : -1.18 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 557 TYR 0.026 0.001 TYR H 32 PHE 0.017 0.002 PHE H 67 TRP 0.065 0.002 TRP L 35 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00298 (21101) covalent geometry : angle 0.79851 (28630) SS BOND : bond 0.00283 ( 34) SS BOND : angle 2.03223 ( 68) hydrogen bonds : bond 0.04141 ( 688) hydrogen bonds : angle 5.49691 ( 2016) Misc. bond : bond 0.00285 ( 1) link_ALPHA1-2 : bond 0.00766 ( 6) link_ALPHA1-2 : angle 1.68911 ( 18) link_ALPHA1-3 : bond 0.01142 ( 16) link_ALPHA1-3 : angle 1.59099 ( 48) link_ALPHA1-6 : bond 0.00886 ( 14) link_ALPHA1-6 : angle 1.86377 ( 42) link_BETA1-2 : bond 0.00255 ( 8) link_BETA1-2 : angle 1.76361 ( 24) link_BETA1-4 : bond 0.00392 ( 96) link_BETA1-4 : angle 2.07056 ( 288) link_BETA1-6 : bond 0.00326 ( 9) link_BETA1-6 : angle 1.25463 ( 27) link_NAG-ASN : bond 0.00392 ( 64) link_NAG-ASN : angle 3.25394 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8813 (tpp) cc_final: 0.8339 (tpp) REVERT: A 122 LEU cc_start: 0.9031 (mm) cc_final: 0.8828 (mm) REVERT: A 217 TYR cc_start: 0.8207 (m-80) cc_final: 0.7636 (m-80) REVERT: A 425 ASN cc_start: 0.8339 (t0) cc_final: 0.8128 (t0) REVERT: A 484 TYR cc_start: 0.8730 (p90) cc_final: 0.8523 (p90) REVERT: B 587 LEU cc_start: 0.9492 (mt) cc_final: 0.9088 (tp) REVERT: B 629 MET cc_start: 0.8182 (tpp) cc_final: 0.7557 (tpp) REVERT: C 100 MET cc_start: 0.8680 (mtm) cc_final: 0.8386 (mtm) REVERT: C 297 THR cc_start: 0.8067 (p) cc_final: 0.7831 (p) REVERT: C 373 MET cc_start: 0.8726 (mmm) cc_final: 0.8307 (mmm) REVERT: C 482 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8486 (mm-30) REVERT: D 530 MET cc_start: 0.7623 (mtp) cc_final: 0.7236 (ttm) REVERT: D 647 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7606 (mp0) REVERT: E 45 TRP cc_start: 0.7964 (m-90) cc_final: 0.7726 (m-90) REVERT: E 318 TYR cc_start: 0.8248 (m-80) cc_final: 0.7841 (m-80) REVERT: E 484 TYR cc_start: 0.8852 (p90) cc_final: 0.8313 (p90) REVERT: F 534 SER cc_start: 0.8937 (p) cc_final: 0.8259 (p) REVERT: F 535 MET cc_start: 0.7885 (mpp) cc_final: 0.7465 (mpp) REVERT: H 45 LEU cc_start: 0.8820 (mt) cc_final: 0.8463 (mt) REVERT: H 72 ASP cc_start: 0.7669 (t70) cc_final: 0.7318 (t0) REVERT: H 77 THR cc_start: 0.8151 (p) cc_final: 0.7331 (p) REVERT: H 79 TYR cc_start: 0.8078 (m-80) cc_final: 0.7388 (m-10) REVERT: H 98 GLU cc_start: 0.7427 (tt0) cc_final: 0.6734 (tt0) REVERT: H 100 MET cc_start: 0.7796 (pmm) cc_final: 0.7493 (pmm) REVERT: L 82 ASP cc_start: 0.7553 (m-30) cc_final: 0.7299 (m-30) REVERT: M 100 MET cc_start: 0.9087 (mpp) cc_final: 0.8603 (mpp) REVERT: N 27 GLU cc_start: 0.8673 (tp30) cc_final: 0.8181 (tp30) REVERT: N 45 GLN cc_start: 0.8422 (mm110) cc_final: 0.7783 (mm110) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1171 time to fit residues: 54.9471 Evaluate side-chains 207 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 140 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS B 551 GLN B 563 GLN B 577 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** N 27DGLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.078565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.060568 restraints weight = 68308.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063193 restraints weight = 40506.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.063789 restraints weight = 25640.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.063804 restraints weight = 22554.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.064011 restraints weight = 22611.110| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21349 Z= 0.213 Angle : 0.920 29.143 29337 Z= 0.411 Chirality : 0.051 0.478 3850 Planarity : 0.004 0.042 3338 Dihedral : 9.164 60.617 6745 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.64 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.17), residues: 2243 helix: 0.19 (0.25), residues: 431 sheet: -0.46 (0.20), residues: 636 loop : -1.15 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 633 TYR 0.021 0.002 TYR H 32 PHE 0.013 0.002 PHE C 53 TRP 0.079 0.003 TRP L 35 HIS 0.008 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00469 (21101) covalent geometry : angle 0.85000 (28630) SS BOND : bond 0.00532 ( 34) SS BOND : angle 2.27467 ( 68) hydrogen bonds : bond 0.04432 ( 688) hydrogen bonds : angle 5.50763 ( 2016) Misc. bond : bond 0.00304 ( 1) link_ALPHA1-2 : bond 0.00727 ( 6) link_ALPHA1-2 : angle 1.64719 ( 18) link_ALPHA1-3 : bond 0.01135 ( 16) link_ALPHA1-3 : angle 1.65281 ( 48) link_ALPHA1-6 : bond 0.00817 ( 14) link_ALPHA1-6 : angle 1.84497 ( 42) link_BETA1-2 : bond 0.00382 ( 8) link_BETA1-2 : angle 1.93939 ( 24) link_BETA1-4 : bond 0.00363 ( 96) link_BETA1-4 : angle 2.05394 ( 288) link_BETA1-6 : bond 0.00452 ( 9) link_BETA1-6 : angle 1.68353 ( 27) link_NAG-ASN : bond 0.00460 ( 64) link_NAG-ASN : angle 3.29384 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8816 (ppp) cc_final: 0.8407 (ppp) REVERT: A 104 MET cc_start: 0.8840 (tpp) cc_final: 0.8359 (tpt) REVERT: A 122 LEU cc_start: 0.9048 (mm) cc_final: 0.8781 (mm) REVERT: A 217 TYR cc_start: 0.8063 (m-80) cc_final: 0.7442 (m-80) REVERT: A 425 ASN cc_start: 0.8332 (t0) cc_final: 0.8111 (t0) REVERT: B 629 MET cc_start: 0.8123 (tpp) cc_final: 0.7575 (tpp) REVERT: C 297 THR cc_start: 0.8234 (p) cc_final: 0.7917 (p) REVERT: C 373 MET cc_start: 0.8767 (mmm) cc_final: 0.8541 (mmp) REVERT: C 482 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8533 (mm-30) REVERT: D 565 MET cc_start: 0.8082 (tpt) cc_final: 0.7570 (tmm) REVERT: E 318 TYR cc_start: 0.8304 (m-80) cc_final: 0.8018 (m-80) REVERT: E 484 TYR cc_start: 0.8855 (p90) cc_final: 0.8286 (p90) REVERT: F 534 SER cc_start: 0.9083 (p) cc_final: 0.8225 (p) REVERT: F 535 MET cc_start: 0.7891 (mpp) cc_final: 0.7499 (mpp) REVERT: F 629 MET cc_start: 0.8207 (mtt) cc_final: 0.6838 (mtt) REVERT: H 72 ASP cc_start: 0.7786 (t70) cc_final: 0.7377 (t0) REVERT: H 77 THR cc_start: 0.8183 (p) cc_final: 0.7348 (p) REVERT: H 79 TYR cc_start: 0.8211 (m-80) cc_final: 0.7492 (m-10) REVERT: H 98 GLU cc_start: 0.7462 (tt0) cc_final: 0.7001 (tt0) REVERT: H 100 MET cc_start: 0.8044 (pmm) cc_final: 0.7586 (pmm) REVERT: L 81 GLU cc_start: 0.7901 (tp30) cc_final: 0.7611 (pp20) REVERT: M 100 MET cc_start: 0.9050 (mpp) cc_final: 0.8778 (mpp) REVERT: N 27 GLU cc_start: 0.8669 (tp30) cc_final: 0.8202 (tp30) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1145 time to fit residues: 49.0018 Evaluate side-chains 193 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 96 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060696 restraints weight = 68221.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.062477 restraints weight = 41194.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.063657 restraints weight = 29948.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064406 restraints weight = 24537.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.064767 restraints weight = 21681.481| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21349 Z= 0.178 Angle : 0.882 24.685 29337 Z= 0.397 Chirality : 0.050 0.471 3850 Planarity : 0.004 0.079 3338 Dihedral : 8.860 58.260 6745 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.46 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.17), residues: 2243 helix: 0.09 (0.25), residues: 438 sheet: -0.46 (0.20), residues: 614 loop : -1.21 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 557 TYR 0.013 0.001 TYR E 435 PHE 0.013 0.001 PHE L 85 TRP 0.078 0.002 TRP E 45 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00387 (21101) covalent geometry : angle 0.80930 (28630) SS BOND : bond 0.00301 ( 34) SS BOND : angle 2.07875 ( 68) hydrogen bonds : bond 0.04253 ( 688) hydrogen bonds : angle 5.46488 ( 2016) Misc. bond : bond 0.00269 ( 1) link_ALPHA1-2 : bond 0.00729 ( 6) link_ALPHA1-2 : angle 1.73250 ( 18) link_ALPHA1-3 : bond 0.01105 ( 16) link_ALPHA1-3 : angle 1.65617 ( 48) link_ALPHA1-6 : bond 0.00801 ( 14) link_ALPHA1-6 : angle 1.74318 ( 42) link_BETA1-2 : bond 0.00281 ( 8) link_BETA1-2 : angle 1.80962 ( 24) link_BETA1-4 : bond 0.00369 ( 96) link_BETA1-4 : angle 1.97217 ( 288) link_BETA1-6 : bond 0.00287 ( 9) link_BETA1-6 : angle 1.43628 ( 27) link_NAG-ASN : bond 0.00401 ( 64) link_NAG-ASN : angle 3.39407 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8807 (ppp) cc_final: 0.8397 (ppp) REVERT: A 104 MET cc_start: 0.8919 (tpp) cc_final: 0.8492 (tpp) REVERT: A 217 TYR cc_start: 0.8172 (m-80) cc_final: 0.7636 (m-80) REVERT: A 425 ASN cc_start: 0.8415 (t0) cc_final: 0.8175 (t0) REVERT: B 629 MET cc_start: 0.8251 (tpp) cc_final: 0.7644 (tpp) REVERT: C 100 MET cc_start: 0.8495 (mtm) cc_final: 0.8068 (mtm) REVERT: C 104 MET cc_start: 0.9106 (tmm) cc_final: 0.8891 (tmm) REVERT: C 297 THR cc_start: 0.8134 (p) cc_final: 0.7805 (p) REVERT: C 373 MET cc_start: 0.8726 (mmm) cc_final: 0.8520 (mmp) REVERT: C 482 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8489 (mm-30) REVERT: D 530 MET cc_start: 0.7764 (mtp) cc_final: 0.7158 (mtm) REVERT: E 318 TYR cc_start: 0.8320 (m-80) cc_final: 0.8025 (m-80) REVERT: E 484 TYR cc_start: 0.8829 (p90) cc_final: 0.8291 (p90) REVERT: F 629 MET cc_start: 0.7906 (mtt) cc_final: 0.7509 (mtt) REVERT: H 45 LEU cc_start: 0.8860 (mt) cc_final: 0.8425 (mt) REVERT: H 72 ASP cc_start: 0.7697 (t70) cc_final: 0.7416 (t0) REVERT: H 77 THR cc_start: 0.8224 (p) cc_final: 0.7539 (p) REVERT: H 79 TYR cc_start: 0.8245 (m-80) cc_final: 0.7622 (m-10) REVERT: H 100 MET cc_start: 0.7942 (pmm) cc_final: 0.7483 (pmm) REVERT: M 100 MET cc_start: 0.9022 (mpp) cc_final: 0.8771 (mpp) REVERT: N 3 VAL cc_start: 0.7387 (t) cc_final: 0.7165 (t) REVERT: N 4 MET cc_start: 0.7189 (mmp) cc_final: 0.6593 (tpp) REVERT: N 27 GLU cc_start: 0.8667 (tp30) cc_final: 0.8200 (tp30) REVERT: N 45 GLN cc_start: 0.7857 (mp10) cc_final: 0.7585 (mp10) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1166 time to fit residues: 50.3884 Evaluate side-chains 192 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN E 374 HIS ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.080175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.062003 restraints weight = 67745.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.063813 restraints weight = 40662.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.065010 restraints weight = 29498.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.065769 restraints weight = 24052.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.066282 restraints weight = 21223.097| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21349 Z= 0.144 Angle : 0.864 26.757 29337 Z= 0.390 Chirality : 0.050 0.456 3850 Planarity : 0.004 0.071 3338 Dihedral : 8.488 58.058 6745 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.38 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.17), residues: 2243 helix: 0.14 (0.25), residues: 437 sheet: -0.38 (0.20), residues: 633 loop : -1.23 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 633 TYR 0.010 0.001 TYR E 435 PHE 0.011 0.001 PHE L 85 TRP 0.101 0.002 TRP E 45 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00303 (21101) covalent geometry : angle 0.79731 (28630) SS BOND : bond 0.00321 ( 34) SS BOND : angle 2.11856 ( 68) hydrogen bonds : bond 0.04099 ( 688) hydrogen bonds : angle 5.38983 ( 2016) Misc. bond : bond 0.00243 ( 1) link_ALPHA1-2 : bond 0.00764 ( 6) link_ALPHA1-2 : angle 1.79138 ( 18) link_ALPHA1-3 : bond 0.01110 ( 16) link_ALPHA1-3 : angle 1.56665 ( 48) link_ALPHA1-6 : bond 0.00828 ( 14) link_ALPHA1-6 : angle 1.70436 ( 42) link_BETA1-2 : bond 0.00212 ( 8) link_BETA1-2 : angle 1.71506 ( 24) link_BETA1-4 : bond 0.00388 ( 96) link_BETA1-4 : angle 1.88680 ( 288) link_BETA1-6 : bond 0.00314 ( 9) link_BETA1-6 : angle 1.30156 ( 27) link_NAG-ASN : bond 0.00362 ( 64) link_NAG-ASN : angle 3.21033 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8781 (ppp) cc_final: 0.8483 (ppp) REVERT: A 104 MET cc_start: 0.8828 (tpp) cc_final: 0.8414 (tpp) REVERT: A 217 TYR cc_start: 0.8077 (m-80) cc_final: 0.7547 (m-80) REVERT: A 425 ASN cc_start: 0.8274 (t0) cc_final: 0.8068 (t0) REVERT: B 565 MET cc_start: 0.6296 (ttm) cc_final: 0.5896 (tmm) REVERT: B 629 MET cc_start: 0.8165 (tpp) cc_final: 0.7568 (tpp) REVERT: C 100 MET cc_start: 0.8616 (mtm) cc_final: 0.8184 (mtm) REVERT: C 104 MET cc_start: 0.9088 (tmm) cc_final: 0.8871 (tmm) REVERT: C 107 ASP cc_start: 0.8221 (t70) cc_final: 0.7979 (t70) REVERT: C 297 THR cc_start: 0.8004 (p) cc_final: 0.7704 (p) REVERT: C 482 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8473 (mm-30) REVERT: E 191 TYR cc_start: 0.8274 (m-80) cc_final: 0.7992 (m-80) REVERT: E 318 TYR cc_start: 0.8309 (m-80) cc_final: 0.8010 (m-80) REVERT: E 484 TYR cc_start: 0.8861 (p90) cc_final: 0.8300 (p90) REVERT: F 530 MET cc_start: 0.8133 (mmm) cc_final: 0.7655 (tpp) REVERT: F 536 THR cc_start: 0.8585 (m) cc_final: 0.8235 (p) REVERT: F 591 GLN cc_start: 0.8748 (tt0) cc_final: 0.8414 (tp-100) REVERT: H 45 LEU cc_start: 0.8819 (mt) cc_final: 0.8305 (mt) REVERT: H 72 ASP cc_start: 0.7704 (t70) cc_final: 0.7366 (t0) REVERT: H 77 THR cc_start: 0.8230 (p) cc_final: 0.7543 (p) REVERT: H 79 TYR cc_start: 0.8233 (m-80) cc_final: 0.7607 (m-10) REVERT: H 100 MET cc_start: 0.7889 (pmm) cc_final: 0.7466 (pmm) REVERT: L 39 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7906 (mmmm) REVERT: L 82 ASP cc_start: 0.7774 (m-30) cc_final: 0.7290 (m-30) REVERT: M 100 MET cc_start: 0.9021 (mpp) cc_final: 0.8747 (mpp) REVERT: N 3 VAL cc_start: 0.7321 (t) cc_final: 0.7090 (t) REVERT: N 4 MET cc_start: 0.7019 (mmp) cc_final: 0.6452 (tpp) REVERT: N 27 GLU cc_start: 0.8677 (tp30) cc_final: 0.8192 (tp30) REVERT: N 45 GLN cc_start: 0.7787 (mp10) cc_final: 0.7382 (mp10) REVERT: N 81 GLU cc_start: 0.7921 (pm20) cc_final: 0.7686 (pm20) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1203 time to fit residues: 53.6063 Evaluate side-chains 200 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 163 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 221 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.061486 restraints weight = 68010.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.063256 restraints weight = 41108.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064446 restraints weight = 29898.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065184 restraints weight = 24413.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065683 restraints weight = 21568.839| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21349 Z= 0.160 Angle : 0.873 29.351 29337 Z= 0.394 Chirality : 0.050 0.459 3850 Planarity : 0.004 0.067 3338 Dihedral : 8.292 55.935 6745 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.33 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.17), residues: 2243 helix: 0.17 (0.25), residues: 433 sheet: -0.35 (0.20), residues: 596 loop : -1.23 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 633 TYR 0.012 0.001 TYR E 435 PHE 0.014 0.001 PHE L 85 TRP 0.079 0.002 TRP E 45 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00346 (21101) covalent geometry : angle 0.80580 (28630) SS BOND : bond 0.00519 ( 34) SS BOND : angle 2.43773 ( 68) hydrogen bonds : bond 0.04144 ( 688) hydrogen bonds : angle 5.37552 ( 2016) Misc. bond : bond 0.00260 ( 1) link_ALPHA1-2 : bond 0.00743 ( 6) link_ALPHA1-2 : angle 1.74864 ( 18) link_ALPHA1-3 : bond 0.01090 ( 16) link_ALPHA1-3 : angle 1.53982 ( 48) link_ALPHA1-6 : bond 0.00804 ( 14) link_ALPHA1-6 : angle 1.72015 ( 42) link_BETA1-2 : bond 0.00256 ( 8) link_BETA1-2 : angle 1.72665 ( 24) link_BETA1-4 : bond 0.00371 ( 96) link_BETA1-4 : angle 1.89849 ( 288) link_BETA1-6 : bond 0.00303 ( 9) link_BETA1-6 : angle 1.47279 ( 27) link_NAG-ASN : bond 0.00355 ( 64) link_NAG-ASN : angle 3.14887 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8761 (ppp) cc_final: 0.8468 (ppp) REVERT: A 104 MET cc_start: 0.8857 (tpp) cc_final: 0.8408 (tpp) REVERT: A 217 TYR cc_start: 0.7884 (m-80) cc_final: 0.7412 (m-80) REVERT: A 425 ASN cc_start: 0.8226 (t0) cc_final: 0.7912 (t0) REVERT: A 475 MET cc_start: 0.8477 (tpp) cc_final: 0.8271 (tpt) REVERT: B 565 MET cc_start: 0.6250 (ttm) cc_final: 0.5734 (tmm) REVERT: B 629 MET cc_start: 0.8144 (tpp) cc_final: 0.7569 (tpp) REVERT: C 100 MET cc_start: 0.8629 (mtm) cc_final: 0.8213 (mtm) REVERT: C 297 THR cc_start: 0.8023 (p) cc_final: 0.7746 (p) REVERT: C 373 MET cc_start: 0.8436 (tpp) cc_final: 0.8210 (tpt) REVERT: C 482 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8482 (mm-30) REVERT: D 634 GLU cc_start: 0.9012 (tt0) cc_final: 0.8812 (tt0) REVERT: E 191 TYR cc_start: 0.8353 (m-80) cc_final: 0.8055 (m-80) REVERT: E 318 TYR cc_start: 0.8306 (m-80) cc_final: 0.8010 (m-80) REVERT: E 484 TYR cc_start: 0.8885 (p90) cc_final: 0.8267 (p90) REVERT: F 530 MET cc_start: 0.8229 (mmm) cc_final: 0.7672 (tpp) REVERT: F 536 THR cc_start: 0.8510 (m) cc_final: 0.8166 (p) REVERT: F 591 GLN cc_start: 0.8780 (tt0) cc_final: 0.8473 (tp-100) REVERT: H 45 LEU cc_start: 0.8826 (mt) cc_final: 0.8318 (mt) REVERT: H 72 ASP cc_start: 0.7719 (t70) cc_final: 0.7359 (t0) REVERT: H 77 THR cc_start: 0.8280 (p) cc_final: 0.7547 (p) REVERT: H 79 TYR cc_start: 0.8223 (m-80) cc_final: 0.7631 (m-10) REVERT: H 100 MET cc_start: 0.8012 (pmm) cc_final: 0.7664 (pmm) REVERT: L 39 LYS cc_start: 0.8290 (mmtm) cc_final: 0.7921 (mmmm) REVERT: L 82 ASP cc_start: 0.7583 (m-30) cc_final: 0.7325 (m-30) REVERT: M 100 MET cc_start: 0.9051 (mpp) cc_final: 0.8784 (mpp) REVERT: N 3 VAL cc_start: 0.7376 (t) cc_final: 0.7152 (t) REVERT: N 4 MET cc_start: 0.6991 (mmp) cc_final: 0.6372 (tpp) REVERT: N 27 GLU cc_start: 0.8627 (tp30) cc_final: 0.8191 (tp30) REVERT: N 45 GLN cc_start: 0.7918 (mp10) cc_final: 0.7676 (mp10) REVERT: N 81 GLU cc_start: 0.7913 (pm20) cc_final: 0.7656 (pm20) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1144 time to fit residues: 48.6363 Evaluate side-chains 192 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 84 optimal weight: 0.0980 chunk 129 optimal weight: 0.0040 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 GLN M 76 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.062336 restraints weight = 69802.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.063942 restraints weight = 44537.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.065010 restraints weight = 33312.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065738 restraints weight = 27799.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.066172 restraints weight = 24694.231| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21349 Z= 0.170 Angle : 0.874 26.493 29337 Z= 0.397 Chirality : 0.050 0.514 3850 Planarity : 0.004 0.064 3338 Dihedral : 8.226 58.112 6745 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.73 % Favored : 92.82 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.38 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 2243 helix: 0.14 (0.25), residues: 435 sheet: -0.32 (0.20), residues: 604 loop : -1.28 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 557 TYR 0.018 0.001 TYR E 217 PHE 0.011 0.001 PHE C 53 TRP 0.071 0.003 TRP E 45 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00373 (21101) covalent geometry : angle 0.80319 (28630) SS BOND : bond 0.00412 ( 34) SS BOND : angle 2.35589 ( 68) hydrogen bonds : bond 0.04181 ( 688) hydrogen bonds : angle 5.39842 ( 2016) Misc. bond : bond 0.00256 ( 1) link_ALPHA1-2 : bond 0.00726 ( 6) link_ALPHA1-2 : angle 1.78508 ( 18) link_ALPHA1-3 : bond 0.01056 ( 16) link_ALPHA1-3 : angle 1.52180 ( 48) link_ALPHA1-6 : bond 0.00798 ( 14) link_ALPHA1-6 : angle 1.71759 ( 42) link_BETA1-2 : bond 0.00260 ( 8) link_BETA1-2 : angle 1.70499 ( 24) link_BETA1-4 : bond 0.00357 ( 96) link_BETA1-4 : angle 1.88033 ( 288) link_BETA1-6 : bond 0.00294 ( 9) link_BETA1-6 : angle 1.50591 ( 27) link_NAG-ASN : bond 0.00361 ( 64) link_NAG-ASN : angle 3.31890 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.76 seconds wall clock time: 44 minutes 34.67 seconds (2674.67 seconds total)