Starting phenix.real_space_refine on Sat Jul 4 03:26:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fae_28954/07_2026/8fae_28954_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fae_28954/07_2026/8fae_28954.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fae_28954/07_2026/8fae_28954_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fae_28954/07_2026/8fae_28954_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fae_28954/07_2026/8fae_28954.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fae_28954/07_2026/8fae_28954.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 96 5.16 5 C 10949 2.51 5 N 2663 2.21 5 O 3985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17693 Number of models: 1 Model: "" Number of chains: 79 Chain: "B" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1157 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 1, 'TRANS': 143} Chain: "C" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3675 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 22, 'TRANS': 444} Chain breaks: 1 Chain: "D" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1132 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "E" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3675 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 22, 'TRANS': 444} Chain breaks: 1 Chain: "A" Number of atoms: 3684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3684 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 22, 'TRANS': 445} Chain breaks: 1 Chain: "F" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1143 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 1, 'TRANS': 141} 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: 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: "I" 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: "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: "L" 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: "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: 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: "O" 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: "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: 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: "R" 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: "S" 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: "T" 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: "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: 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: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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: "b" 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "f" 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: "g" 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: "h" 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: "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: 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: "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: 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: "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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 53 Unusual residues: {'BMA': 1, 'NAG': 3} 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: "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: "OA" 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: "r" 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: "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: 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: 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: "v" 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: "w" 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: "x" 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: "y" 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: "z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "0" 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: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 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: 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: "4" 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: "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: 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: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" 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: "9" 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: "AA" 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: "BA" 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: "CA" 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: "DA" 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: "EA" 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: "FA" 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: "GA" 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: "HA" 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: "IA" 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: "JA" 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: "KA" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "LA" 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: "MA" 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: "NA" 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: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'83G': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'83G': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'83G': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 4.68, per 1000 atoms: 0.26 Number of scatterers: 17693 At special positions: 0 Unit cell: (146.85, 146.85, 133.65, 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 96 16.00 O 3985 8.00 N 2663 7.00 C 10949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.05 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN T 4 " - " MAN T 5 " " MAN X 4 " - " MAN X 5 " " MAN v 4 " - " MAN v 5 " " MANEA 4 " - " MANEA 5 " " MANOA 4 " - " MANOA 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " BMA 9 3 " - " MAN 9 7 " " MAN 9 4 " - " MAN 9 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA k 3 " - " MAN k 4 " " BMA v 3 " - " MAN v 4 " " BMA w 3 " - " MAN w 4 " " BMAAA 3 " - " MANAA 4 " " BMADA 3 " - " MANDA 4 " " BMAEA 3 " - " MANEA 4 " " BMAGA 3 " - " MANGA 4 " " BMAHA 3 " - " MANHA 4 " " BMAOA 3 " - " MANOA 4 " " MANOA 6 " - " MANOA 7 " ALPHA1-6 " BMA 9 3 " - " MAN 9 4 " " MAN 9 4 " - " MAN 9 6 " " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 7 " " BMA a 3 " - " MAN a 4 " " BMA k 3 " - " MAN k 5 " " BMA u 3 " - " MAN u 4 " " BMA v 3 " - " MAN v 6 " " MAN v 6 " - " MAN v 7 " " BMA y 3 " - " MAN y 4 " " BMAEA 3 " - " MANEA 6 " " MANEA 6 " - " MANEA 7 " " BMAHA 3 " - " MANHA 5 " " BMAOA 3 " - " MANOA 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " 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 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 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 J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " 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 l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " BMA o 3 " - " NAG o 4 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " 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 x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " NAGBA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGGA 2 " - " BMAGA 3 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " " NAGKA 1 " - " NAGKA 2 " " NAGKA 2 " - " BMAKA 3 " " NAGLA 1 " - " NAGLA 2 " " NAGMA 1 " - " NAGMA 2 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGOA 2 " - " BMAOA 3 " BETA1-6 " NAG H 1 " - " FUC H 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 3 " " NAG O 1 " - " FUC O 3 " " NAG Y 1 " - " FUC Y 2 " " NAG e 1 " - " FUC e 4 " " NAG f 1 " - " FUC f 3 " " NAG g 1 " - " FUC g 3 " " NAG m 1 " - " FUC m 3 " " NAG z 1 " - " FUC z 4 " " NAGKA 1 " - " FUCKA 4 " " NAGLA 1 " - " FUCLA 3 " " NAGNA 1 " - " FUCNA 3 " NAG-ASN " NAG 0 1 " - " ASN E 448 " " NAG 1 1 " - " ASN A 88 " " NAG 2 1 " - " ASN A 130 " " NAG 3 1 " - " ASN A 156 " " NAG 4 1 " - " ASN A 160 " " NAG 5 1 " - " ASN A 188 " " NAG 6 1 " - " ASN A 197 " " NAG 7 1 " - " ASN A 234 " " NAG 8 1 " - " ASN A 241 " " NAG 9 1 " - " ASN A 262 " " NAG A 602 " - " ASN A 356 " " NAG C 602 " - " ASN C 397 " " NAG E 602 " - " ASN E 356 " " NAG G 1 " - " ASN B 611 " " NAG H 1 " - " ASN B 616 " " NAG I 1 " - " ASN B 625 " " NAG J 1 " - " ASN B 637 " " NAG K 1 " - " ASN C 88 " " NAG L 1 " - " ASN C 130 " " NAG M 1 " - " ASN C 156 " " NAG N 1 " - " ASN C 160 " " NAG O 1 " - " ASN C 188 " " NAG P 1 " - " ASN C 197 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 241 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 276 " " NAG U 1 " - " ASN C 295 " " NAG V 1 " - " ASN C 301 " " NAG W 1 " - " ASN C 332 " " NAG X 1 " - " ASN C 339 " " NAG Y 1 " - " ASN C 356 " " NAG Z 1 " - " ASN C 362 " " NAG a 1 " - " ASN C 386 " " NAG b 1 " - " ASN C 392 " " NAG c 1 " - " ASN C 401 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN D 611 " " NAG f 1 " - " ASN D 616 " " NAG g 1 " - " ASN D 625 " " NAG h 1 " - " ASN D 637 " " NAG i 1 " - " ASN E 88 " " NAG j 1 " - " ASN E 130 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 160 " " NAG m 1 " - " ASN E 188 " " NAG n 1 " - " ASN E 197 " " NAG o 1 " - " ASN E 234 " " NAG p 1 " - " ASN E 241 " " NAG r 1 " - " ASN E 276 " " NAG s 1 " - " ASN E 295 " " NAG t 1 " - " ASN E 301 " " NAG u 1 " - " ASN E 332 " " NAG v 1 " - " ASN E 339 " " NAG w 1 " - " ASN E 362 " " NAG x 1 " - " ASN E 386 " " NAG y 1 " - " ASN E 392 " " NAG z 1 " - " ASN E 401 " " NAGAA 1 " - " ASN A 276 " " NAGBA 1 " - " ASN A 295 " " NAGCA 1 " - " ASN A 301 " " NAGDA 1 " - " ASN A 332 " " NAGEA 1 " - " ASN A 339 " " NAGFA 1 " - " ASN A 362 " " NAGGA 1 " - " ASN A 386 " " NAGHA 1 " - " ASN A 392 " " NAGIA 1 " - " ASN A 401 " " NAGJA 1 " - " ASN A 448 " " NAGKA 1 " - " ASN F 611 " " NAGLA 1 " - " ASN F 616 " " NAGMA 1 " - " ASN F 625 " " NAGNA 1 " - " ASN F 637 " " NAGOA 1 " - " ASN E 262 " Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 630.5 milliseconds 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 29 sheets defined 29.8% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'B' and resid 536 through 564 removed outlier: 3.536A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 633 Processing helix chain 'B' and resid 634 through 637 removed outlier: 4.545A pdb=" N ASN B 637 " --> pdb=" O GLU B 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.738A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.194A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 459 through 463 removed outlier: 3.716A pdb=" N HIS C 462 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN C 463 " --> pdb=" O ASN C 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 459 through 463' Processing helix chain 'C' and resid 474 through 484 removed outlier: 3.743A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.689A pdb=" N ALA D 526 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 527' Processing helix chain 'D' and resid 529 through 536 removed outlier: 3.599A pdb=" N THR D 536 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 562 removed outlier: 3.565A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 561 " --> pdb=" O LYS D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 removed outlier: 4.024A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.842A pdb=" N LYS D 633 " --> pdb=" O MET D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 661 removed outlier: 4.606A pdb=" N GLY D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU D 641 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 63 removed outlier: 4.037A pdb=" N TYR E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.158A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 334 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.688A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.633A pdb=" N TYR A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.973A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.572A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 334 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 388 through 392 removed outlier: 3.815A pdb=" N ASN A 392 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 464A removed outlier: 3.581A pdb=" N ASP A 464A" --> pdb=" O HIS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.673A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 removed outlier: 3.647A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 536 removed outlier: 4.136A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR F 536 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 547 removed outlier: 3.589A pdb=" N LEU F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY F 547 " --> pdb=" O LEU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 552 removed outlier: 3.667A pdb=" N GLN F 552 " --> pdb=" O ILE F 548 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 567 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.133A pdb=" N LYS F 633 " --> pdb=" O MET F 629 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.330A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.043A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.542A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.978A pdb=" N VAL C 120 " --> pdb=" O GLN C 203 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AA7, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.205A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.762A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.856A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.315A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.315A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.856A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.762A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.163A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 447 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.809A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AB2, first strand: chain 'E' and resid 85 through 86 removed outlier: 4.157A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL E 44 " --> pdb=" O GLU E 492 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU E 494 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL E 42 " --> pdb=" O LEU E 494 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 85 through 86 removed outlier: 4.157A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL E 44 " --> pdb=" O GLU E 492 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU E 494 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL E 42 " --> pdb=" O LEU E 494 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 175 Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.261A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.054A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.745A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.489A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.142A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.732A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 283 through 298 current: chain 'E' and resid 358 through 360 Processing sheet with id=AB9, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.732A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.142A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.489A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.745A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 414 through 415 Processing sheet with id=AC1, first strand: chain 'E' and resid 301 through 303 removed outlier: 3.900A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 306 through 308 Processing sheet with id=AC3, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.349A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC6, first strand: chain 'A' and resid 170 through 174 Processing sheet with id=AC7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.303A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.737A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 359 through 361 Processing sheet with id=AC9, first strand: chain 'A' and resid 271 through 274 removed outlier: 11.127A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.101A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 443 through 456 current: chain 'A' and resid 414 through 415 Processing sheet with id=AD1, first strand: chain 'A' and resid 301 through 308 removed outlier: 6.569A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 374 through 378 548 hydrogen bonds defined for protein. 1551 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: 3.42 Time building geometry restraints manager: 3.30 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: 3337 1.33 - 1.45: 4760 1.45 - 1.57: 9756 1.57 - 1.69: 9 1.69 - 1.81: 132 Bond restraints: 17994 Sorted by residual: bond pdb=" N LEU D 568 " pdb=" CA LEU D 568 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.49e+01 bond pdb=" N VAL B 608 " pdb=" CA VAL B 608 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.50e-03 1.78e+04 2.07e+01 bond pdb=" C5 BMA T 3 " pdb=" O5 BMA T 3 " ideal model delta sigma weight residual 1.417 1.496 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sigma weight residual 1.417 1.496 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 BMA r 3 " pdb=" O5 BMA r 3 " ideal model delta sigma weight residual 1.417 1.496 -0.079 2.00e-02 2.50e+03 1.54e+01 ... (remaining 17989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 22425 2.86 - 5.71: 1891 5.71 - 8.57: 115 8.57 - 11.42: 12 11.42 - 14.28: 6 Bond angle restraints: 24449 Sorted by residual: angle pdb=" N LEU D 565 " pdb=" CA LEU D 565 " pdb=" C LEU D 565 " ideal model delta sigma weight residual 113.28 105.14 8.14 1.22e+00 6.72e-01 4.45e+01 angle pdb=" N TRP D 571 " pdb=" CA TRP D 571 " pdb=" C TRP D 571 " ideal model delta sigma weight residual 114.56 106.63 7.93 1.27e+00 6.20e-01 3.89e+01 angle pdb=" CA ASN C 362 " pdb=" CB ASN C 362 " pdb=" CG ASN C 362 " ideal model delta sigma weight residual 112.60 118.56 -5.96 1.00e+00 1.00e+00 3.56e+01 angle pdb=" CA ASN D 611 " pdb=" CB ASN D 611 " pdb=" CG ASN D 611 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.16e+01 angle pdb=" N TRP A 479 " pdb=" CA TRP A 479 " pdb=" C TRP A 479 " ideal model delta sigma weight residual 113.55 106.48 7.07 1.26e+00 6.30e-01 3.14e+01 ... (remaining 24444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.44: 12681 28.44 - 56.89: 644 56.89 - 85.33: 316 85.33 - 113.78: 309 113.78 - 142.22: 22 Dihedral angle restraints: 13972 sinusoidal: 8674 harmonic: 5298 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 9.52 83.48 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS E 228 " pdb=" SG CYS E 228 " pdb=" SG CYS E 239 " pdb=" CB CYS E 239 " ideal model delta sinusoidal sigma weight residual 93.00 158.04 -65.04 1 1.00e+01 1.00e-02 5.55e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -140.49 54.49 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 13969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 3312 0.219 - 0.439: 181 0.439 - 0.658: 12 0.658 - 0.877: 5 0.877 - 1.097: 4 Chirality restraints: 3514 Sorted by residual: chirality pdb=" C1 NAG 6 2 " pdb=" O4 NAG 6 1 " pdb=" C2 NAG 6 2 " pdb=" O5 NAG 6 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-02 2.50e+03 8.32e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-02 2.50e+03 7.95e+02 chirality pdb=" C1 BMA 4 3 " pdb=" O4 NAG 4 2 " pdb=" C2 BMA 4 3 " pdb=" O5 BMA 4 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.66e+02 ... (remaining 3511 not shown) Planarity restraints: 2797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG 6 2 " 0.342 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG 6 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG 6 2 " 0.053 2.00e-02 2.50e+03 pdb=" N2 NAG 6 2 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG 6 2 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG o 2 " 0.329 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG o 2 " -0.074 2.00e-02 2.50e+03 pdb=" C8 NAG o 2 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG o 2 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NAG o 2 " 0.140 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.326 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG i 2 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.112 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.509 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.143 2.00e-02 2.50e+03 ... (remaining 2794 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2153 2.76 - 3.30: 18084 3.30 - 3.83: 28980 3.83 - 4.37: 37274 4.37 - 4.90: 55610 Nonbonded interactions: 142101 Sorted by model distance: nonbonded pdb=" O6 MANOA 6 " pdb=" C1 MANOA 8 " model vdw 2.228 3.470 nonbonded pdb=" O ARG D 579 " pdb=" OG1 THR D 582 " model vdw 2.249 3.040 nonbonded pdb=" O ILE A 225 " pdb=" OG1 THR A 244 " model vdw 2.318 3.040 nonbonded pdb=" OE1 GLU A 211 " pdb=" O3 NAG 9 1 " model vdw 2.328 3.040 nonbonded pdb=" O ILE E 333 " pdb=" N ILE E 414 " model vdw 2.352 3.120 ... (remaining 142096 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' and resid 1 through 2) selection = (chain '1' and resid 1 through 2) selection = (chain '2' and resid 1 through 2) selection = (chain '4' and resid 1 through 2) selection = (chain '6' and resid 1 through 2) selection = (chain '8' and resid 1 through 2) selection = (chain 'BA' and resid 1 through 2) selection = (chain 'CA' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'IA' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'JA' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'LA' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'NA' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'V' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'h' 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 'p' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) selection = (chain 's' and resid 1 through 2) selection = (chain 't' and resid 1 through 2) selection = (chain 'x' and resid 1 through 2) } ncs_group { reference = (chain '3' and resid 1 through 3) selection = (chain 'AA' and resid 1 through 3) selection = (chain 'DA' and resid 1 through 3) selection = (chain 'GA' and resid 1 through 3) selection = (chain 'KA' and resid 1 through 3) selection = (chain 'a' and resid 1 through 3) selection = (chain 'e' and resid 1 through 3) selection = (chain 'o' and resid 1 through 3) selection = (chain 'u' and resid 1 through 3) selection = (chain 'w' and resid 1 through 3) selection = (chain 'y' and resid 1 through 3) selection = (chain 'z' and resid 1 through 3) } ncs_group { reference = (chain '5' and resid 1) selection = (chain '7' and resid 1) selection = (chain 'FA' and resid 1) selection = (chain 'MA' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) selection = (chain 'c' and resid 1) selection = (chain 'l' and resid 1) } ncs_group { reference = (chain '9' and resid 5 through 7) selection = (chain 'EA' and resid 5 through 7) selection = (chain 'OA' and resid 6 through 8) selection = (chain 'S' and resid 4 through 6) selection = (chain 'X' and resid 5 through 7) selection = (chain 'v' and resid 5 through 7) } ncs_group { reference = (chain 'A' and resid 33 through 602) selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 520 through 661) selection = chain 'D' selection = (chain 'F' and resid 520 through 661) } ncs_group { reference = chain 'HA' selection = chain 'T' selection = chain 'W' selection = chain 'k' } 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: 0.430 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.680 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.050 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:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 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 : 0.013 0.099 18270 Z= 0.856 Angle : 1.763 23.188 25247 Z= 1.056 Chirality : 0.121 1.097 3514 Planarity : 0.035 0.295 2724 Dihedral : 25.842 142.225 10452 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.94 % Allowed : 8.49 % Favored : 90.57 % Rotamer: Outliers : 5.71 % Allowed : 9.52 % Favored : 84.77 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.19), residues: 1814 helix: 0.06 (0.25), residues: 466 sheet: -1.44 (0.27), residues: 326 loop : -1.61 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 469 TYR 0.017 0.002 TYR E 173 PHE 0.023 0.002 PHE C 383 TRP 0.026 0.003 TRP A 395 HIS 0.005 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.01271 / 0.86 (17994) covalent geometry : angle 1.63204 / 1.04 (24449) SS BOND : bond 0.00686 / 0.46 ( 30) SS BOND : angle 1.61854 / 1.03 ( 60) hydrogen bonds : bond 0.19712 / 13.58 ( 516) hydrogen bonds : angle 9.07328 / 6.47 ( 1551) link_ALPHA1-2 : bond 0.01107 / 0.60 ( 6) link_ALPHA1-2 : angle 2.40667 / 1.48 ( 18) link_ALPHA1-3 : bond 0.01690 / 0.84 ( 17) link_ALPHA1-3 : angle 3.71151 / 2.36 ( 51) link_ALPHA1-6 : bond 0.00677 / 0.41 ( 16) link_ALPHA1-6 : angle 2.27649 / 1.46 ( 48) link_BETA1-4 : bond 0.00936 / 0.63 ( 122) link_BETA1-4 : angle 3.84630 / 2.62 ( 366) link_BETA1-6 : bond 0.00254 / 0.11 ( 12) link_BETA1-6 : angle 1.64756 / 0.93 ( 36) link_NAG-ASN : bond 0.01574 / 1.14 ( 73) link_NAG-ASN : angle 5.48348 / 4.26 ( 219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 436 time to evaluate : 0.770 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: B 530 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.6426 (ptm) REVERT: B 580 VAL cc_start: 0.9321 (t) cc_final: 0.8614 (t) REVERT: B 584 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8371 (mt-10) REVERT: B 589 ASP cc_start: 0.9416 (m-30) cc_final: 0.9009 (m-30) REVERT: B 595 ILE cc_start: 0.9230 (mm) cc_final: 0.8988 (mm) REVERT: B 605 THR cc_start: 0.9133 (p) cc_final: 0.8792 (t) REVERT: B 630 GLU cc_start: 0.9544 (mt-10) cc_final: 0.9043 (mt-10) REVERT: B 634 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8965 (mp0) REVERT: B 649 SER cc_start: 0.8867 (p) cc_final: 0.8521 (p) REVERT: B 651 ASN cc_start: 0.8818 (m-40) cc_final: 0.8240 (m110) REVERT: C 66 HIS cc_start: 0.8255 (m-70) cc_final: 0.7800 (m90) REVERT: C 97 LYS cc_start: 0.9418 (mptt) cc_final: 0.9045 (mmtm) REVERT: C 107 ASP cc_start: 0.8379 (m-30) cc_final: 0.8149 (m-30) REVERT: C 109 ILE cc_start: 0.9363 (mt) cc_final: 0.8960 (mm) REVERT: C 233 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8006 (t80) REVERT: C 255 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8620 (t) REVERT: C 279 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.7882 (p0) REVERT: C 280 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.7875 (t0) REVERT: C 342 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9124 (mt) REVERT: C 359 ILE cc_start: 0.9081 (mp) cc_final: 0.8800 (mm) REVERT: C 373 MET cc_start: 0.7583 (mtp) cc_final: 0.7030 (ttp) REVERT: C 425 ASN cc_start: 0.9209 (m-40) cc_final: 0.9004 (t0) REVERT: C 447 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7965 (t) REVERT: D 523 LEU cc_start: 0.8287 (mt) cc_final: 0.7810 (pp) REVERT: D 627 THR cc_start: 0.9060 (OUTLIER) cc_final: 0.8564 (t) REVERT: D 630 GLU cc_start: 0.9090 (pt0) cc_final: 0.8544 (pt0) REVERT: D 648 GLU cc_start: 0.9102 (pp20) cc_final: 0.8871 (pp20) REVERT: D 650 GLN cc_start: 0.9306 (tp40) cc_final: 0.8774 (tm-30) REVERT: D 654 GLU cc_start: 0.8894 (tp30) cc_final: 0.8527 (tp30) REVERT: E 57 ASP cc_start: 0.8006 (t0) cc_final: 0.7452 (p0) REVERT: E 80 ASN cc_start: 0.9249 (p0) cc_final: 0.9041 (t0) REVERT: E 86 LEU cc_start: 0.9765 (mp) cc_final: 0.9509 (mp) REVERT: E 120 VAL cc_start: 0.8969 (t) cc_final: 0.8763 (t) REVERT: E 172 ASP cc_start: 0.8539 (m-30) cc_final: 0.8329 (m-30) REVERT: E 318 TYR cc_start: 0.8406 (m-10) cc_final: 0.8133 (m-80) REVERT: E 381 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6944 (mt-10) REVERT: E 393 SER cc_start: 0.7054 (OUTLIER) cc_final: 0.6541 (p) REVERT: E 403 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8273 (p) REVERT: E 475 MET cc_start: 0.7994 (mmm) cc_final: 0.7516 (mmp) REVERT: E 491 ILE cc_start: 0.9559 (mt) cc_final: 0.9297 (mp) REVERT: E 492 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7430 (pm20) REVERT: E 500 LYS cc_start: 0.8218 (mtpp) cc_final: 0.8011 (mmtt) REVERT: A 35 TRP cc_start: 0.8604 (m100) cc_final: 0.8347 (m100) REVERT: A 98 ASN cc_start: 0.8855 (t0) cc_final: 0.8575 (t0) REVERT: A 104 MET cc_start: 0.7999 (ppp) cc_final: 0.7736 (ppp) REVERT: A 107 ASP cc_start: 0.8684 (m-30) cc_final: 0.8448 (m-30) REVERT: A 210 PHE cc_start: 0.8405 (m-80) cc_final: 0.7856 (m-80) REVERT: A 229 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7783 (tptp) REVERT: A 240 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8637 (ttpt) REVERT: A 279 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: A 342 LEU cc_start: 0.8535 (mt) cc_final: 0.8014 (mt) REVERT: A 349 LEU cc_start: 0.9299 (mt) cc_final: 0.9091 (mt) REVERT: A 377 ASN cc_start: 0.8644 (p0) cc_final: 0.8416 (t0) REVERT: A 381 GLU cc_start: 0.7959 (mm-30) cc_final: 0.6949 (mt-10) REVERT: A 383 PHE cc_start: 0.8394 (m-10) cc_final: 0.8128 (m-10) REVERT: A 477 ASP cc_start: 0.9277 (m-30) cc_final: 0.8979 (m-30) REVERT: F 538 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.8943 (t) REVERT: F 539 VAL cc_start: 0.9587 (t) cc_final: 0.9358 (p) REVERT: F 546 SER cc_start: 0.7250 (p) cc_final: 0.6934 (p) REVERT: F 579 ARG cc_start: 0.8716 (mtp85) cc_final: 0.7796 (mmm-85) REVERT: F 580 VAL cc_start: 0.9299 (t) cc_final: 0.8801 (m) REVERT: F 589 ASP cc_start: 0.8954 (m-30) cc_final: 0.8538 (m-30) REVERT: F 618 THR cc_start: 0.8904 (p) cc_final: 0.8392 (t) REVERT: F 626 MET cc_start: 0.8373 (tpt) cc_final: 0.7144 (tpp) REVERT: F 629 MET cc_start: 0.9095 (mmm) cc_final: 0.8243 (tpt) REVERT: F 647 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8614 (mt-10) REVERT: F 648 GLU cc_start: 0.9180 (pp20) cc_final: 0.8907 (pp20) outliers start: 93 outliers final: 20 residues processed: 505 average time/residue: 0.1262 time to fit residues: 95.8096 Evaluate side-chains 294 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 621 MET Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 137 VAL Chi-restraints excluded: chain E residue 145 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 381 GLU Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 653 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN C 82 GLN D 575 GLN D 591 GLN D 624 ASN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 HIS ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.084875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.064770 restraints weight = 61413.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.066911 restraints weight = 33362.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.068343 restraints weight = 23396.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.069205 restraints weight = 18934.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.069743 restraints weight = 16714.952| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18270 Z= 0.220 Angle : 1.093 13.324 25247 Z= 0.460 Chirality : 0.058 0.892 3514 Planarity : 0.005 0.080 2724 Dihedral : 21.517 136.649 7029 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.01 % Favored : 93.83 % Rotamer: Outliers : 4.30 % Allowed : 16.40 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.19), residues: 1814 helix: 0.03 (0.23), residues: 473 sheet: -1.12 (0.25), residues: 410 loop : -1.35 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 151 TYR 0.024 0.002 TYR E 173 PHE 0.013 0.001 PHE E 382 TRP 0.040 0.002 TRP F 571 HIS 0.007 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (17994) covalent geometry : angle 0.98359 / 0.43 (24449) SS BOND : bond 0.00480 / 0.25 ( 30) SS BOND : angle 1.06643 / 0.63 ( 60) hydrogen bonds : bond 0.05488 / 3.70 ( 516) hydrogen bonds : angle 6.35064 / 4.55 ( 1551) link_ALPHA1-2 : bond 0.00829 / 0.43 ( 6) link_ALPHA1-2 : angle 2.31042 / 1.44 ( 18) link_ALPHA1-3 : bond 0.02157 / 1.14 ( 17) link_ALPHA1-3 : angle 3.19317 / 1.96 ( 51) link_ALPHA1-6 : bond 0.00650 / 0.41 ( 16) link_ALPHA1-6 : angle 1.66074 / 1.01 ( 48) link_BETA1-4 : bond 0.00919 / 0.66 ( 122) link_BETA1-4 : angle 3.13875 / 2.26 ( 366) link_BETA1-6 : bond 0.00580 / 0.28 ( 12) link_BETA1-6 : angle 1.66274 / 0.95 ( 36) link_NAG-ASN : bond 0.00480 / 0.31 ( 73) link_NAG-ASN : angle 2.99488 / 2.31 ( 219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 255 time to evaluate : 0.599 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: B 530 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6313 (ptm) REVERT: B 584 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8494 (mp0) REVERT: B 589 ASP cc_start: 0.8969 (m-30) cc_final: 0.8635 (m-30) REVERT: B 595 ILE cc_start: 0.9324 (mm) cc_final: 0.8736 (mm) REVERT: B 626 MET cc_start: 0.8233 (tpp) cc_final: 0.7947 (tpp) REVERT: B 629 MET cc_start: 0.8822 (tpp) cc_final: 0.8514 (tpp) REVERT: B 630 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8676 (mt-10) REVERT: B 647 GLU cc_start: 0.8913 (pt0) cc_final: 0.8597 (pp20) REVERT: C 66 HIS cc_start: 0.7685 (m-70) cc_final: 0.7370 (m90) REVERT: C 185 ASP cc_start: 0.8652 (m-30) cc_final: 0.8130 (t0) REVERT: C 233 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8890 (t80) REVERT: C 373 MET cc_start: 0.7937 (mtp) cc_final: 0.7480 (ttm) REVERT: C 447 SER cc_start: 0.9330 (OUTLIER) cc_final: 0.9102 (m) REVERT: D 523 LEU cc_start: 0.7876 (mt) cc_final: 0.7266 (pp) REVERT: D 575 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8490 (pp30) REVERT: D 588 ARG cc_start: 0.9051 (ptt90) cc_final: 0.8540 (ptt-90) REVERT: D 615 SER cc_start: 0.9341 (t) cc_final: 0.9085 (p) REVERT: D 626 MET cc_start: 0.7243 (tpp) cc_final: 0.6996 (tpp) REVERT: D 630 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8836 (pt0) REVERT: D 647 GLU cc_start: 0.9332 (pp20) cc_final: 0.8702 (pp20) REVERT: E 57 ASP cc_start: 0.8008 (t0) cc_final: 0.7509 (p0) REVERT: E 80 ASN cc_start: 0.8815 (p0) cc_final: 0.8570 (t0) REVERT: E 98 ASN cc_start: 0.8507 (t0) cc_final: 0.8189 (t0) REVERT: E 104 MET cc_start: 0.9382 (ttm) cc_final: 0.8924 (tmm) REVERT: E 381 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7420 (mt-10) REVERT: E 434 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8005 (tmm) REVERT: A 35 TRP cc_start: 0.8594 (m100) cc_final: 0.8391 (m100) REVERT: A 98 ASN cc_start: 0.9233 (t0) cc_final: 0.8907 (t0) REVERT: A 104 MET cc_start: 0.8291 (ppp) cc_final: 0.7707 (ppp) REVERT: A 107 ASP cc_start: 0.8353 (m-30) cc_final: 0.8133 (m-30) REVERT: A 229 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.7811 (tptp) REVERT: A 240 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8756 (ttpt) REVERT: A 291 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8880 (t) REVERT: A 349 LEU cc_start: 0.9466 (mt) cc_final: 0.9196 (mt) REVERT: A 381 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7217 (mt-10) REVERT: A 383 PHE cc_start: 0.8858 (m-10) cc_final: 0.8587 (m-10) REVERT: F 522 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7916 (t80) REVERT: F 538 THR cc_start: 0.9630 (OUTLIER) cc_final: 0.8069 (p) REVERT: F 579 ARG cc_start: 0.9037 (mtp85) cc_final: 0.8715 (mmm-85) REVERT: F 583 VAL cc_start: 0.9662 (t) cc_final: 0.9404 (p) REVERT: F 589 ASP cc_start: 0.8816 (m-30) cc_final: 0.8433 (m-30) REVERT: F 601 LYS cc_start: 0.7478 (mtmm) cc_final: 0.6962 (mtmm) REVERT: F 621 MET cc_start: 0.8499 (tpp) cc_final: 0.8060 (tpp) REVERT: F 629 MET cc_start: 0.9338 (mmm) cc_final: 0.9120 (tpp) REVERT: F 648 GLU cc_start: 0.9162 (pp20) cc_final: 0.8923 (pp20) outliers start: 70 outliers final: 34 residues processed: 307 average time/residue: 0.1282 time to fit residues: 60.2933 Evaluate side-chains 256 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 211 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 GLU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 575 GLN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 567 LYS Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 596 TRP Chi-restraints excluded: chain F residue 630 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 2 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 136 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 GLN ** F 656 ASN ** 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 = 0.3586 r_free = 0.3586 target = 0.082816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062262 restraints weight = 62580.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064372 restraints weight = 34478.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.065756 restraints weight = 24477.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066610 restraints weight = 19943.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067124 restraints weight = 17687.835| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18270 Z= 0.222 Angle : 0.999 14.185 25247 Z= 0.423 Chirality : 0.055 0.634 3514 Planarity : 0.004 0.056 2724 Dihedral : 17.164 128.943 6995 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.95 % Favored : 92.94 % Rotamer: Outliers : 4.73 % Allowed : 18.24 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1814 helix: 0.17 (0.23), residues: 475 sheet: -0.99 (0.25), residues: 402 loop : -1.26 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 298 TYR 0.012 0.002 TYR D 586 PHE 0.011 0.001 PHE C 396 TRP 0.029 0.002 TRP F 596 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (17994) covalent geometry : angle 0.90130 / 0.40 (24449) SS BOND : bond 0.00468 / 0.21 ( 30) SS BOND : angle 1.35605 / 0.76 ( 60) hydrogen bonds : bond 0.05047 / 3.41 ( 516) hydrogen bonds : angle 5.85096 / 4.24 ( 1551) link_ALPHA1-2 : bond 0.00752 / 0.38 ( 6) link_ALPHA1-2 : angle 2.39405 / 1.45 ( 18) link_ALPHA1-3 : bond 0.01884 / 0.97 ( 17) link_ALPHA1-3 : angle 3.22264 / 1.91 ( 51) link_ALPHA1-6 : bond 0.00756 / 0.43 ( 16) link_ALPHA1-6 : angle 1.62047 / 0.96 ( 48) link_BETA1-4 : bond 0.00836 / 0.59 ( 122) link_BETA1-4 : angle 2.88749 / 2.08 ( 366) link_BETA1-6 : bond 0.00592 / 0.25 ( 12) link_BETA1-6 : angle 1.77434 / 1.01 ( 36) link_NAG-ASN : bond 0.00333 / 0.21 ( 73) link_NAG-ASN : angle 2.45912 / 1.84 ( 219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 236 time to evaluate : 0.593 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: B 530 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6236 (ptp) REVERT: B 554 ASN cc_start: 0.8854 (m-40) cc_final: 0.8387 (p0) REVERT: B 556 LEU cc_start: 0.8914 (mt) cc_final: 0.8682 (mt) REVERT: B 560 GLU cc_start: 0.7669 (tp30) cc_final: 0.7402 (tm-30) REVERT: B 584 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8427 (mt-10) REVERT: B 589 ASP cc_start: 0.8894 (m-30) cc_final: 0.8537 (m-30) REVERT: B 606 THR cc_start: 0.8955 (m) cc_final: 0.8186 (m) REVERT: B 643 TYR cc_start: 0.9024 (m-10) cc_final: 0.8723 (m-10) REVERT: B 654 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8846 (mp0) REVERT: C 66 HIS cc_start: 0.7806 (m-70) cc_final: 0.7551 (m90) REVERT: C 95 MET cc_start: 0.8884 (ppp) cc_final: 0.8430 (ppp) REVERT: C 342 LEU cc_start: 0.9703 (mt) cc_final: 0.9450 (mt) REVERT: C 373 MET cc_start: 0.8062 (mtp) cc_final: 0.7311 (ttm) REVERT: C 423 ILE cc_start: 0.9423 (mt) cc_final: 0.9017 (pt) REVERT: C 426 MET cc_start: 0.8339 (tpp) cc_final: 0.7729 (mmm) REVERT: D 523 LEU cc_start: 0.8087 (mt) cc_final: 0.7524 (pp) REVERT: D 529 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8946 (t) REVERT: D 557 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9020 (pptt) REVERT: D 588 ARG cc_start: 0.9126 (ptt90) cc_final: 0.8785 (ptt-90) REVERT: D 591 GLN cc_start: 0.9352 (mt0) cc_final: 0.9075 (mt0) REVERT: D 626 MET cc_start: 0.7503 (tpp) cc_final: 0.6090 (tpp) REVERT: D 627 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8359 (t) REVERT: D 629 MET cc_start: 0.8434 (tpt) cc_final: 0.8156 (tpt) REVERT: D 630 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: D 634 GLU cc_start: 0.8645 (pm20) cc_final: 0.8427 (pm20) REVERT: D 647 GLU cc_start: 0.9249 (pp20) cc_final: 0.8739 (pp20) REVERT: D 650 GLN cc_start: 0.9397 (tp40) cc_final: 0.8868 (tp-100) REVERT: E 57 ASP cc_start: 0.7937 (t0) cc_final: 0.7500 (p0) REVERT: E 98 ASN cc_start: 0.8452 (t0) cc_final: 0.8203 (t0) REVERT: E 104 MET cc_start: 0.9259 (ttm) cc_final: 0.9052 (ttm) REVERT: E 381 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 35 TRP cc_start: 0.8779 (m100) cc_final: 0.8474 (m100) REVERT: A 98 ASN cc_start: 0.9306 (t0) cc_final: 0.8985 (t0) REVERT: A 107 ASP cc_start: 0.8402 (m-30) cc_final: 0.8201 (m-30) REVERT: A 229 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.7857 (tptp) REVERT: A 260 LEU cc_start: 0.9002 (mt) cc_final: 0.8768 (mp) REVERT: A 381 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7428 (mt-10) REVERT: A 383 PHE cc_start: 0.9141 (m-10) cc_final: 0.8867 (m-10) REVERT: F 522 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7697 (t80) REVERT: F 579 ARG cc_start: 0.9180 (mtp85) cc_final: 0.8631 (mtm-85) REVERT: F 583 VAL cc_start: 0.9673 (t) cc_final: 0.9375 (p) REVERT: F 589 ASP cc_start: 0.8717 (m-30) cc_final: 0.8379 (m-30) REVERT: F 601 LYS cc_start: 0.7838 (mtmm) cc_final: 0.7341 (mtmm) REVERT: F 602 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7627 (pt) REVERT: F 621 MET cc_start: 0.8531 (tpp) cc_final: 0.8044 (tpp) REVERT: F 626 MET cc_start: 0.7665 (tpp) cc_final: 0.7432 (tpp) REVERT: F 633 LYS cc_start: 0.9139 (mmmm) cc_final: 0.8799 (mmtm) REVERT: F 643 TYR cc_start: 0.9051 (m-10) cc_final: 0.8606 (m-10) outliers start: 77 outliers final: 44 residues processed: 293 average time/residue: 0.1233 time to fit residues: 54.7893 Evaluate side-chains 257 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 557 LYS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 630 GLU Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 596 TRP Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 630 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 104 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 159 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 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 = 0.3618 r_free = 0.3618 target = 0.084456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.064114 restraints weight = 61606.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.066282 restraints weight = 33521.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.067686 restraints weight = 23532.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068578 restraints weight = 19115.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069126 restraints weight = 16833.916| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18270 Z= 0.158 Angle : 0.913 12.694 25247 Z= 0.387 Chirality : 0.052 0.628 3514 Planarity : 0.004 0.055 2724 Dihedral : 14.919 127.098 6987 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.06 % Favored : 93.83 % Rotamer: Outliers : 3.87 % Allowed : 19.78 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.19), residues: 1814 helix: 0.32 (0.23), residues: 477 sheet: -0.85 (0.25), residues: 412 loop : -1.20 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 503 TYR 0.017 0.001 TYR B 586 PHE 0.013 0.001 PHE C 233 TRP 0.028 0.002 TRP F 596 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (17994) covalent geometry : angle 0.82212 / 0.37 (24449) SS BOND : bond 0.00316 / 0.16 ( 30) SS BOND : angle 0.98260 / 0.52 ( 60) hydrogen bonds : bond 0.04617 / 3.10 ( 516) hydrogen bonds : angle 5.51925 / 3.98 ( 1551) link_ALPHA1-2 : bond 0.00789 / 0.40 ( 6) link_ALPHA1-2 : angle 2.49736 / 1.51 ( 18) link_ALPHA1-3 : bond 0.01924 / 1.04 ( 17) link_ALPHA1-3 : angle 3.29676 / 1.94 ( 51) link_ALPHA1-6 : bond 0.00795 / 0.45 ( 16) link_ALPHA1-6 : angle 1.53777 / 0.92 ( 48) link_BETA1-4 : bond 0.00803 / 0.57 ( 122) link_BETA1-4 : angle 2.65414 / 1.93 ( 366) link_BETA1-6 : bond 0.00586 / 0.29 ( 12) link_BETA1-6 : angle 1.51683 / 0.87 ( 36) link_NAG-ASN : bond 0.00313 / 0.21 ( 73) link_NAG-ASN : angle 2.16562 / 1.62 ( 219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 228 time to evaluate : 0.623 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: B 556 LEU cc_start: 0.8919 (mt) cc_final: 0.8691 (mt) REVERT: B 560 GLU cc_start: 0.7515 (tp30) cc_final: 0.7281 (tm-30) REVERT: B 584 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8402 (mt-10) REVERT: B 589 ASP cc_start: 0.8820 (m-30) cc_final: 0.8433 (m-30) REVERT: B 626 MET cc_start: 0.8265 (tpp) cc_final: 0.7685 (tpp) REVERT: B 630 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8486 (pt0) REVERT: B 654 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8496 (mt-10) REVERT: C 66 HIS cc_start: 0.7851 (m-70) cc_final: 0.7562 (m90) REVERT: C 113 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8415 (m-30) REVERT: C 342 LEU cc_start: 0.9677 (mt) cc_final: 0.9429 (mt) REVERT: C 373 MET cc_start: 0.7956 (mtp) cc_final: 0.7659 (ttm) REVERT: C 423 ILE cc_start: 0.9405 (mt) cc_final: 0.9016 (pt) REVERT: C 469 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8296 (mtp85) REVERT: D 523 LEU cc_start: 0.8648 (mt) cc_final: 0.8084 (pp) REVERT: D 557 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8972 (pptt) REVERT: D 568 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6088 (mm) REVERT: D 588 ARG cc_start: 0.9059 (ptt90) cc_final: 0.8420 (ptt-90) REVERT: D 591 GLN cc_start: 0.9299 (mt0) cc_final: 0.9087 (mt0) REVERT: D 647 GLU cc_start: 0.9246 (pp20) cc_final: 0.8861 (pp20) REVERT: E 57 ASP cc_start: 0.7817 (t0) cc_final: 0.7460 (p0) REVERT: E 95 MET cc_start: 0.9272 (ppp) cc_final: 0.8932 (ppp) REVERT: E 381 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7506 (mt-10) REVERT: E 400 TRP cc_start: 0.6000 (t60) cc_final: 0.5640 (t60) REVERT: E 426 MET cc_start: 0.8500 (mmm) cc_final: 0.8248 (mmm) REVERT: E 434 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8106 (tmm) REVERT: A 35 TRP cc_start: 0.8619 (m100) cc_final: 0.8310 (m100) REVERT: A 98 ASN cc_start: 0.9349 (t0) cc_final: 0.8920 (t0) REVERT: A 151 ARG cc_start: 0.7897 (mpt180) cc_final: 0.5970 (mmp80) REVERT: A 229 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.7757 (tptp) REVERT: A 255 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.9163 (t) REVERT: A 381 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7393 (mt-10) REVERT: A 383 PHE cc_start: 0.9110 (m-10) cc_final: 0.8856 (m-10) REVERT: F 522 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.7436 (t80) REVERT: F 530 MET cc_start: 0.8892 (mmm) cc_final: 0.8381 (mmm) REVERT: F 579 ARG cc_start: 0.9160 (mtp85) cc_final: 0.8573 (mtm-85) REVERT: F 589 ASP cc_start: 0.8732 (m-30) cc_final: 0.8338 (m-30) REVERT: F 601 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7286 (mtmm) REVERT: F 621 MET cc_start: 0.8464 (tpp) cc_final: 0.8221 (tpp) REVERT: F 643 TYR cc_start: 0.9148 (m-10) cc_final: 0.8458 (m-10) REVERT: F 647 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8362 (mt-10) REVERT: F 648 GLU cc_start: 0.9091 (pp20) cc_final: 0.8881 (pp20) REVERT: F 655 LYS cc_start: 0.8570 (ptpp) cc_final: 0.8333 (ptpp) outliers start: 63 outliers final: 38 residues processed: 278 average time/residue: 0.1204 time to fit residues: 51.2026 Evaluate side-chains 250 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 557 LYS Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 596 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 99 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 178 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 553 ASN B 554 ASN B 564 HIS B 591 GLN B 653 GLN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN E 280 ASN E 460 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS A 389 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.080271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.059642 restraints weight = 63003.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061613 restraints weight = 35153.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.062901 restraints weight = 25336.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.063660 restraints weight = 20918.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.064140 restraints weight = 18760.513| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 18270 Z= 0.330 Angle : 1.013 13.865 25247 Z= 0.441 Chirality : 0.053 0.606 3514 Planarity : 0.004 0.048 2724 Dihedral : 13.962 135.636 6984 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.72 % Favored : 92.17 % Rotamer: Outliers : 5.47 % Allowed : 19.84 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 are not related in a simple way. whole: -1.18 (0.19), residues: 1814 helix: 0.28 (0.24), residues: 463 sheet: -0.82 (0.26), residues: 380 loop : -1.27 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 542 TYR 0.012 0.002 TYR C 40 PHE 0.016 0.002 PHE C 468 TRP 0.046 0.003 TRP F 571 HIS 0.005 0.002 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.33 (17994) covalent geometry : angle 0.92591 / 0.42 (24449) SS BOND : bond 0.00401 / 0.22 ( 30) SS BOND : angle 1.57385 / 0.83 ( 60) hydrogen bonds : bond 0.04956 / 3.40 ( 516) hydrogen bonds : angle 5.63073 / 4.09 ( 1551) link_ALPHA1-2 : bond 0.00648 / 0.33 ( 6) link_ALPHA1-2 : angle 2.39148 / 1.46 ( 18) link_ALPHA1-3 : bond 0.01784 / 0.95 ( 17) link_ALPHA1-3 : angle 3.38098 / 1.93 ( 51) link_ALPHA1-6 : bond 0.00815 / 0.45 ( 16) link_ALPHA1-6 : angle 1.70160 / 1.04 ( 48) link_BETA1-4 : bond 0.00768 / 0.54 ( 122) link_BETA1-4 : angle 2.68201 / 1.95 ( 366) link_BETA1-6 : bond 0.00630 / 0.27 ( 12) link_BETA1-6 : angle 2.08345 / 1.21 ( 36) link_NAG-ASN : bond 0.00539 / 0.36 ( 73) link_NAG-ASN : angle 2.34064 / 1.71 ( 219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 195 time to evaluate : 0.582 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: B 560 GLU cc_start: 0.7621 (tp30) cc_final: 0.7253 (tm-30) REVERT: B 584 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8466 (mt-10) REVERT: B 589 ASP cc_start: 0.8820 (m-30) cc_final: 0.8467 (m-30) REVERT: B 626 MET cc_start: 0.8482 (tpp) cc_final: 0.7513 (tpp) REVERT: B 655 LYS cc_start: 0.9263 (pptt) cc_final: 0.8985 (pptt) REVERT: C 95 MET cc_start: 0.9296 (ppp) cc_final: 0.8903 (ppp) REVERT: C 373 MET cc_start: 0.8429 (mtp) cc_final: 0.7840 (ttm) REVERT: C 381 GLU cc_start: 0.8738 (tp30) cc_final: 0.8457 (tp30) REVERT: C 469 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8560 (mtp85) REVERT: D 530 MET cc_start: 0.9076 (mtp) cc_final: 0.8629 (mtp) REVERT: D 588 ARG cc_start: 0.9127 (ptt90) cc_final: 0.8688 (ptt-90) REVERT: D 636 ASP cc_start: 0.9230 (t0) cc_final: 0.8988 (t0) REVERT: D 647 GLU cc_start: 0.9105 (pp20) cc_final: 0.8766 (pp20) REVERT: E 57 ASP cc_start: 0.7973 (t0) cc_final: 0.7616 (p0) REVERT: E 95 MET cc_start: 0.9384 (ppp) cc_final: 0.9002 (ppp) REVERT: E 381 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7573 (mt-10) REVERT: A 39 TYR cc_start: 0.8679 (m-10) cc_final: 0.8371 (m-10) REVERT: A 104 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7722 (tmm) REVERT: A 151 ARG cc_start: 0.7688 (mpt180) cc_final: 0.6643 (mmp80) REVERT: A 381 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7858 (tp30) REVERT: A 383 PHE cc_start: 0.9179 (m-10) cc_final: 0.8846 (m-10) REVERT: A 454 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9324 (mm) REVERT: F 522 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7242 (t80) REVERT: F 530 MET cc_start: 0.8953 (mmm) cc_final: 0.8714 (mmm) REVERT: F 579 ARG cc_start: 0.9236 (mtp85) cc_final: 0.8694 (mtm-85) REVERT: F 583 VAL cc_start: 0.9702 (t) cc_final: 0.9382 (p) REVERT: F 589 ASP cc_start: 0.8696 (m-30) cc_final: 0.8337 (m-30) REVERT: F 601 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7795 (mtmm) REVERT: F 621 MET cc_start: 0.8697 (tpp) cc_final: 0.8334 (tpp) REVERT: F 647 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8402 (mt-10) REVERT: F 655 LYS cc_start: 0.8417 (ptpp) cc_final: 0.8205 (ptpp) outliers start: 89 outliers final: 60 residues processed: 264 average time/residue: 0.1259 time to fit residues: 50.2970 Evaluate side-chains 247 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 557 LYS Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 139 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 390 LEU Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 596 TRP Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 630 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 93 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 131 optimal weight: 0.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 554 ASN B 653 GLN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 ASN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 550 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 = 0.3586 r_free = 0.3586 target = 0.082406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061893 restraints weight = 61386.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.063921 restraints weight = 34270.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065248 restraints weight = 24542.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066067 restraints weight = 20148.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066546 restraints weight = 17928.816| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18270 Z= 0.163 Angle : 0.891 12.120 25247 Z= 0.383 Chirality : 0.050 0.543 3514 Planarity : 0.004 0.039 2724 Dihedral : 12.952 131.183 6977 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.90 % Favored : 93.99 % Rotamer: Outliers : 3.56 % Allowed : 21.68 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.45 % Twisted General : 0.11 % 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 are not related in a simple way. whole: -1.21 (0.19), residues: 1814 helix: 0.19 (0.24), residues: 469 sheet: -0.87 (0.26), residues: 380 loop : -1.24 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 503 TYR 0.026 0.001 TYR B 586 PHE 0.011 0.001 PHE C 233 TRP 0.030 0.002 TRP F 596 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (17994) covalent geometry : angle 0.80842 / 0.36 (24449) SS BOND : bond 0.00328 / 0.17 ( 30) SS BOND : angle 1.55322 / 0.78 ( 60) hydrogen bonds : bond 0.04495 / 3.08 ( 516) hydrogen bonds : angle 5.43790 / 3.92 ( 1551) link_ALPHA1-2 : bond 0.00766 / 0.38 ( 6) link_ALPHA1-2 : angle 2.57792 / 1.56 ( 18) link_ALPHA1-3 : bond 0.01943 / 1.03 ( 17) link_ALPHA1-3 : angle 3.38983 / 1.97 ( 51) link_ALPHA1-6 : bond 0.00811 / 0.47 ( 16) link_ALPHA1-6 : angle 1.62855 / 1.03 ( 48) link_BETA1-4 : bond 0.00722 / 0.51 ( 122) link_BETA1-4 : angle 2.42203 / 1.78 ( 366) link_BETA1-6 : bond 0.00613 / 0.28 ( 12) link_BETA1-6 : angle 1.69837 / 0.98 ( 36) link_NAG-ASN : bond 0.00266 / 0.18 ( 73) link_NAG-ASN : angle 1.94581 / 1.44 ( 219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 0.501 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: B 584 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8401 (mt-10) REVERT: B 589 ASP cc_start: 0.8736 (m-30) cc_final: 0.8369 (m-30) REVERT: B 629 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7706 (mtm) REVERT: B 654 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8495 (mp0) REVERT: C 95 MET cc_start: 0.9233 (ppp) cc_final: 0.8637 (ppp) REVERT: C 104 MET cc_start: 0.9277 (tmm) cc_final: 0.8937 (tmm) REVERT: C 113 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8510 (m-30) REVERT: C 342 LEU cc_start: 0.9708 (mt) cc_final: 0.9495 (mt) REVERT: C 373 MET cc_start: 0.8078 (mtp) cc_final: 0.7778 (ttm) REVERT: C 381 GLU cc_start: 0.8811 (tp30) cc_final: 0.8515 (tp30) REVERT: C 469 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8431 (mtp85) REVERT: D 557 LYS cc_start: 0.9400 (ttpp) cc_final: 0.8978 (pptt) REVERT: D 588 ARG cc_start: 0.9091 (ptt90) cc_final: 0.8762 (ptt-90) REVERT: D 647 GLU cc_start: 0.9137 (pp20) cc_final: 0.8850 (pp20) REVERT: E 57 ASP cc_start: 0.7718 (t0) cc_final: 0.7479 (p0) REVERT: E 95 MET cc_start: 0.9229 (ppp) cc_final: 0.8844 (ppp) REVERT: E 340 ASN cc_start: 0.8977 (p0) cc_final: 0.8435 (m-40) REVERT: E 381 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7466 (mt-10) REVERT: E 400 TRP cc_start: 0.5989 (t60) cc_final: 0.5773 (t60) REVERT: E 475 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8339 (mmm) REVERT: A 35 TRP cc_start: 0.8844 (m100) cc_final: 0.8413 (m100) REVERT: A 104 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7532 (tmm) REVERT: A 122 LEU cc_start: 0.9339 (mp) cc_final: 0.9125 (mp) REVERT: A 381 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7464 (mt-10) REVERT: A 383 PHE cc_start: 0.9088 (m-10) cc_final: 0.8837 (m-10) REVERT: F 522 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.6995 (t80) REVERT: F 579 ARG cc_start: 0.9214 (mtp85) cc_final: 0.8770 (mtm-85) REVERT: F 589 ASP cc_start: 0.8683 (m-30) cc_final: 0.8389 (m-30) REVERT: F 601 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7866 (mtmm) REVERT: F 621 MET cc_start: 0.8561 (tpp) cc_final: 0.8233 (tpp) REVERT: F 647 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8408 (mt-10) outliers start: 58 outliers final: 44 residues processed: 248 average time/residue: 0.1173 time to fit residues: 44.7285 Evaluate side-chains 239 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 177 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN C 105 HIS ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** 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 = 0.3563 r_free = 0.3563 target = 0.081288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.060598 restraints weight = 62257.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.062582 restraints weight = 35009.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.063888 restraints weight = 25253.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.064704 restraints weight = 20854.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.065187 restraints weight = 18580.578| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18270 Z= 0.202 Angle : 0.903 12.300 25247 Z= 0.391 Chirality : 0.049 0.512 3514 Planarity : 0.004 0.040 2724 Dihedral : 12.398 131.157 6977 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.56 % Favored : 93.33 % Rotamer: Outliers : 4.12 % Allowed : 21.68 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 are not related in a simple way. whole: -1.10 (0.19), residues: 1814 helix: 0.26 (0.24), residues: 457 sheet: -0.80 (0.26), residues: 373 loop : -1.15 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 503 TYR 0.018 0.001 TYR D 586 PHE 0.010 0.001 PHE A 383 TRP 0.030 0.002 TRP F 596 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (17994) covalent geometry : angle 0.82070 / 0.37 (24449) SS BOND : bond 0.00327 / 0.17 ( 30) SS BOND : angle 1.68072 / 0.95 ( 60) hydrogen bonds : bond 0.04456 / 3.04 ( 516) hydrogen bonds : angle 5.43762 / 3.95 ( 1551) link_ALPHA1-2 : bond 0.00679 / 0.34 ( 6) link_ALPHA1-2 : angle 2.49858 / 1.53 ( 18) link_ALPHA1-3 : bond 0.01907 / 1.01 ( 17) link_ALPHA1-3 : angle 3.42212 / 1.96 ( 51) link_ALPHA1-6 : bond 0.00768 / 0.44 ( 16) link_ALPHA1-6 : angle 1.72826 / 1.09 ( 48) link_BETA1-4 : bond 0.00715 / 0.50 ( 122) link_BETA1-4 : angle 2.42269 / 1.78 ( 366) link_BETA1-6 : bond 0.00581 / 0.27 ( 12) link_BETA1-6 : angle 1.83432 / 1.06 ( 36) link_NAG-ASN : bond 0.00294 / 0.19 ( 73) link_NAG-ASN : angle 1.93299 / 1.42 ( 219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 191 time to evaluate : 0.439 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: B 560 GLU cc_start: 0.7466 (tp30) cc_final: 0.7046 (tm-30) REVERT: B 584 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8384 (mt-10) REVERT: B 589 ASP cc_start: 0.8798 (m-30) cc_final: 0.8441 (m-30) REVERT: B 639 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8535 (p) REVERT: B 650 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: C 95 MET cc_start: 0.9179 (ppp) cc_final: 0.8802 (ppp) REVERT: C 113 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8604 (m-30) REVERT: C 381 GLU cc_start: 0.8870 (tp30) cc_final: 0.8548 (tp30) REVERT: C 426 MET cc_start: 0.8755 (mmm) cc_final: 0.8255 (tpp) REVERT: C 469 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8417 (mtp85) REVERT: D 588 ARG cc_start: 0.9067 (ptt90) cc_final: 0.8449 (ptt180) REVERT: D 626 MET cc_start: 0.7754 (tpp) cc_final: 0.7495 (tpp) REVERT: D 647 GLU cc_start: 0.9143 (pp20) cc_final: 0.8861 (pp20) REVERT: E 57 ASP cc_start: 0.7764 (t0) cc_final: 0.7498 (p0) REVERT: E 95 MET cc_start: 0.9247 (ppp) cc_final: 0.8864 (ppp) REVERT: E 340 ASN cc_start: 0.8958 (p0) cc_final: 0.8334 (m-40) REVERT: E 381 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 35 TRP cc_start: 0.8937 (m100) cc_final: 0.8478 (m100) REVERT: A 104 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7571 (tmm) REVERT: A 381 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7776 (tp30) REVERT: A 383 PHE cc_start: 0.9085 (m-10) cc_final: 0.8686 (m-10) REVERT: A 454 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9291 (mm) REVERT: F 522 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.6852 (t80) REVERT: F 530 MET cc_start: 0.8892 (mmm) cc_final: 0.8466 (mmm) REVERT: F 579 ARG cc_start: 0.9252 (mtp85) cc_final: 0.8717 (mtm-85) REVERT: F 589 ASP cc_start: 0.8787 (m-30) cc_final: 0.8447 (m-30) REVERT: F 601 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7747 (ptpp) REVERT: F 621 MET cc_start: 0.8587 (tpp) cc_final: 0.8273 (tpp) REVERT: F 629 MET cc_start: 0.9205 (mmm) cc_final: 0.8771 (tpt) REVERT: F 647 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8374 (mt-10) outliers start: 67 outliers final: 51 residues processed: 242 average time/residue: 0.1114 time to fit residues: 41.7661 Evaluate side-chains 238 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 180 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 630 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 165 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 64 optimal weight: 0.0970 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN A 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.082943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.062690 restraints weight = 61335.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.064789 restraints weight = 33820.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.066103 restraints weight = 23973.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.066970 restraints weight = 19654.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.067500 restraints weight = 17399.484| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18270 Z= 0.149 Angle : 0.880 11.526 25247 Z= 0.379 Chirality : 0.048 0.468 3514 Planarity : 0.003 0.039 2724 Dihedral : 11.628 127.120 6977 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 3.75 % Allowed : 21.93 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 1814 helix: 0.29 (0.24), residues: 457 sheet: -0.77 (0.26), residues: 395 loop : -1.12 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 327 TYR 0.019 0.001 TYR D 586 PHE 0.016 0.001 PHE C 396 TRP 0.053 0.002 TRP C 400 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (17994) covalent geometry : angle 0.80069 / 0.36 (24449) SS BOND : bond 0.00421 / 0.18 ( 30) SS BOND : angle 1.57974 / 0.84 ( 60) hydrogen bonds : bond 0.04267 / 2.92 ( 516) hydrogen bonds : angle 5.30892 / 3.85 ( 1551) link_ALPHA1-2 : bond 0.00772 / 0.39 ( 6) link_ALPHA1-2 : angle 2.64818 / 1.61 ( 18) link_ALPHA1-3 : bond 0.02040 / 1.06 ( 17) link_ALPHA1-3 : angle 3.45039 / 2.00 ( 51) link_ALPHA1-6 : bond 0.00814 / 0.47 ( 16) link_ALPHA1-6 : angle 2.09120 / 1.26 ( 48) link_BETA1-4 : bond 0.00723 / 0.51 ( 122) link_BETA1-4 : angle 2.33026 / 1.73 ( 366) link_BETA1-6 : bond 0.00663 / 0.33 ( 12) link_BETA1-6 : angle 1.64386 / 0.95 ( 36) link_NAG-ASN : bond 0.00250 / 0.17 ( 73) link_NAG-ASN : angle 1.76391 / 1.30 ( 219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.573 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: B 584 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 589 ASP cc_start: 0.8864 (m-30) cc_final: 0.8459 (m-30) REVERT: B 626 MET cc_start: 0.8025 (ttm) cc_final: 0.7668 (ttt) REVERT: B 651 ASN cc_start: 0.8422 (m110) cc_final: 0.8105 (m-40) REVERT: B 655 LYS cc_start: 0.9179 (pptt) cc_final: 0.8975 (pptt) REVERT: C 95 MET cc_start: 0.9131 (ppp) cc_final: 0.8742 (ppp) REVERT: C 104 MET cc_start: 0.9181 (tmm) cc_final: 0.8845 (tmm) REVERT: C 113 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8585 (m-30) REVERT: C 373 MET cc_start: 0.7975 (mtp) cc_final: 0.7754 (ttm) REVERT: C 381 GLU cc_start: 0.8855 (tp30) cc_final: 0.8561 (tp30) REVERT: C 426 MET cc_start: 0.8464 (mmm) cc_final: 0.7872 (tpp) REVERT: C 469 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8545 (mtp85) REVERT: D 581 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.8771 (mm) REVERT: D 588 ARG cc_start: 0.9043 (ptt90) cc_final: 0.8430 (ptt180) REVERT: D 626 MET cc_start: 0.7693 (tpp) cc_final: 0.7427 (tpp) REVERT: D 647 GLU cc_start: 0.9177 (pp20) cc_final: 0.8962 (pp20) REVERT: E 95 MET cc_start: 0.9212 (ppp) cc_final: 0.8920 (ppp) REVERT: E 340 ASN cc_start: 0.8952 (p0) cc_final: 0.8467 (m-40) REVERT: E 381 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7467 (mt-10) REVERT: E 426 MET cc_start: 0.7865 (mmm) cc_final: 0.7438 (mmt) REVERT: E 434 MET cc_start: 0.8684 (ttt) cc_final: 0.8426 (ttm) REVERT: E 475 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8342 (mmm) REVERT: A 35 TRP cc_start: 0.8661 (m100) cc_final: 0.8246 (m100) REVERT: A 381 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7413 (mt-10) REVERT: F 522 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.6403 (t80) REVERT: F 530 MET cc_start: 0.8704 (mmm) cc_final: 0.8249 (mmm) REVERT: F 542 ARG cc_start: 0.8595 (ptm-80) cc_final: 0.8147 (ttp80) REVERT: F 579 ARG cc_start: 0.9256 (mtp85) cc_final: 0.8773 (mtm-85) REVERT: F 589 ASP cc_start: 0.8801 (m-30) cc_final: 0.8497 (m-30) REVERT: F 601 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7170 (ptpp) REVERT: F 621 MET cc_start: 0.8550 (tpp) cc_final: 0.8262 (tpp) REVERT: F 629 MET cc_start: 0.9243 (mmm) cc_final: 0.8664 (tpt) REVERT: F 647 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8328 (mt-10) REVERT: F 653 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8475 (tm-30) outliers start: 61 outliers final: 44 residues processed: 243 average time/residue: 0.1148 time to fit residues: 42.9420 Evaluate side-chains 236 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 186 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 662 GLU Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 653 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.081320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.060907 restraints weight = 61775.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.062937 restraints weight = 34518.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064232 restraints weight = 24729.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065034 restraints weight = 20385.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.065531 restraints weight = 18165.550| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18270 Z= 0.196 Angle : 0.878 12.168 25247 Z= 0.382 Chirality : 0.048 0.458 3514 Planarity : 0.004 0.041 2724 Dihedral : 11.170 120.752 6975 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.17 % Favored : 93.72 % Rotamer: Outliers : 3.62 % Allowed : 22.79 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 1814 helix: 0.39 (0.24), residues: 445 sheet: -0.71 (0.26), residues: 385 loop : -1.12 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 504 TYR 0.029 0.001 TYR B 586 PHE 0.026 0.001 PHE A 383 TRP 0.026 0.002 TRP F 596 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (17994) covalent geometry : angle 0.79853 / 0.36 (24449) SS BOND : bond 0.00373 / 0.25 ( 30) SS BOND : angle 1.74570 / 1.02 ( 60) hydrogen bonds : bond 0.04340 / 2.98 ( 516) hydrogen bonds : angle 5.31318 / 3.86 ( 1551) link_ALPHA1-2 : bond 0.00685 / 0.34 ( 6) link_ALPHA1-2 : angle 2.51525 / 1.53 ( 18) link_ALPHA1-3 : bond 0.01864 / 0.99 ( 17) link_ALPHA1-3 : angle 3.32849 / 1.91 ( 51) link_ALPHA1-6 : bond 0.00693 / 0.40 ( 16) link_ALPHA1-6 : angle 1.74578 / 1.07 ( 48) link_BETA1-4 : bond 0.00708 / 0.50 ( 122) link_BETA1-4 : angle 2.34803 / 1.73 ( 366) link_BETA1-6 : bond 0.00643 / 0.30 ( 12) link_BETA1-6 : angle 1.68828 / 0.98 ( 36) link_NAG-ASN : bond 0.00283 / 0.19 ( 73) link_NAG-ASN : angle 1.83790 / 1.34 ( 219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 0.518 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: B 560 GLU cc_start: 0.7531 (tp30) cc_final: 0.7039 (tm-30) REVERT: B 584 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 589 ASP cc_start: 0.8876 (m-30) cc_final: 0.8496 (m-30) REVERT: B 633 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8643 (mmmm) REVERT: B 655 LYS cc_start: 0.9218 (pptt) cc_final: 0.9004 (pptt) REVERT: C 95 MET cc_start: 0.9170 (ppp) cc_final: 0.8858 (ppp) REVERT: C 113 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: C 381 GLU cc_start: 0.8869 (tp30) cc_final: 0.8564 (tp30) REVERT: C 426 MET cc_start: 0.8709 (mmm) cc_final: 0.8076 (tpp) REVERT: C 469 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8568 (mtp85) REVERT: D 581 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.8818 (mm) REVERT: D 588 ARG cc_start: 0.9053 (ptt90) cc_final: 0.8631 (ptt-90) REVERT: D 626 MET cc_start: 0.7876 (tpp) cc_final: 0.7631 (tpp) REVERT: D 647 GLU cc_start: 0.9144 (pp20) cc_final: 0.8913 (pp20) REVERT: E 95 MET cc_start: 0.9219 (ppp) cc_final: 0.8863 (ppp) REVERT: E 340 ASN cc_start: 0.8968 (p0) cc_final: 0.8387 (m-40) REVERT: E 381 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7455 (mt-10) REVERT: E 426 MET cc_start: 0.8060 (mmm) cc_final: 0.7704 (mmm) REVERT: A 35 TRP cc_start: 0.8893 (m100) cc_final: 0.8581 (m100) REVERT: A 104 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7510 (tmm) REVERT: A 381 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8084 (tp30) REVERT: A 383 PHE cc_start: 0.9070 (m-10) cc_final: 0.8828 (m-10) REVERT: F 522 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.6451 (t80) REVERT: F 530 MET cc_start: 0.8792 (mmm) cc_final: 0.8381 (mmm) REVERT: F 579 ARG cc_start: 0.9277 (mtp85) cc_final: 0.8433 (mtm-85) REVERT: F 589 ASP cc_start: 0.8792 (m-30) cc_final: 0.8497 (m-30) REVERT: F 601 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7558 (ptpp) REVERT: F 621 MET cc_start: 0.8572 (tpp) cc_final: 0.8273 (tpp) REVERT: F 629 MET cc_start: 0.9273 (mmm) cc_final: 0.8715 (tpt) REVERT: F 647 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8361 (mt-10) REVERT: F 655 LYS cc_start: 0.8737 (ptpp) cc_final: 0.8456 (ptpp) outliers start: 59 outliers final: 47 residues processed: 235 average time/residue: 0.1149 time to fit residues: 42.0099 Evaluate side-chains 232 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 0.0570 chunk 143 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 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 = 0.3588 r_free = 0.3588 target = 0.082005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061725 restraints weight = 61527.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.063789 restraints weight = 33892.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065147 restraints weight = 24124.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.065963 restraints weight = 19726.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066454 restraints weight = 17542.254| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18270 Z= 0.171 Angle : 0.860 11.016 25247 Z= 0.378 Chirality : 0.047 0.431 3514 Planarity : 0.004 0.042 2724 Dihedral : 10.487 121.095 6975 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.79 % Favored : 94.10 % Rotamer: Outliers : 3.19 % Allowed : 23.59 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.19), residues: 1814 helix: 0.36 (0.24), residues: 445 sheet: -0.58 (0.26), residues: 402 loop : -1.11 (0.20), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 327 TYR 0.030 0.001 TYR B 586 PHE 0.019 0.001 PHE A 383 TRP 0.024 0.002 TRP F 596 HIS 0.010 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (17994) covalent geometry : angle 0.78560 / 0.36 (24449) SS BOND : bond 0.00439 / 0.30 ( 30) SS BOND : angle 1.68869 / 1.02 ( 60) hydrogen bonds : bond 0.04272 / 2.95 ( 516) hydrogen bonds : angle 5.30003 / 3.84 ( 1551) link_ALPHA1-2 : bond 0.00747 / 0.38 ( 6) link_ALPHA1-2 : angle 2.56769 / 1.55 ( 18) link_ALPHA1-3 : bond 0.01903 / 1.00 ( 17) link_ALPHA1-3 : angle 3.17279 / 1.87 ( 51) link_ALPHA1-6 : bond 0.00717 / 0.43 ( 16) link_ALPHA1-6 : angle 1.67236 / 1.02 ( 48) link_BETA1-4 : bond 0.00703 / 0.49 ( 122) link_BETA1-4 : angle 2.27061 / 1.68 ( 366) link_BETA1-6 : bond 0.00551 / 0.27 ( 12) link_BETA1-6 : angle 1.56451 / 0.91 ( 36) link_NAG-ASN : bond 0.00240 / 0.16 ( 73) link_NAG-ASN : angle 1.72395 / 1.26 ( 219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3628 Ramachandran restraints generated. 1814 Oldfield, 0 Emsley, 1814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.569 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: B 560 GLU cc_start: 0.7395 (tp30) cc_final: 0.6957 (tm-30) REVERT: B 584 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8403 (mt-10) REVERT: B 589 ASP cc_start: 0.8853 (m-30) cc_final: 0.8451 (m-30) REVERT: B 595 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.9003 (mt) REVERT: B 633 LYS cc_start: 0.8950 (ttmm) cc_final: 0.8593 (mmmm) REVERT: C 95 MET cc_start: 0.9163 (ppp) cc_final: 0.8823 (ppp) REVERT: C 104 MET cc_start: 0.9170 (tmm) cc_final: 0.8869 (tmm) REVERT: C 113 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8618 (m-30) REVERT: C 373 MET cc_start: 0.8068 (mtp) cc_final: 0.7824 (ttm) REVERT: C 381 GLU cc_start: 0.8735 (tp30) cc_final: 0.8232 (tm-30) REVERT: C 426 MET cc_start: 0.8566 (mmm) cc_final: 0.8041 (tpp) REVERT: C 469 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8573 (mtp85) REVERT: D 542 ARG cc_start: 0.6978 (mmt-90) cc_final: 0.4718 (mmt-90) REVERT: D 588 ARG cc_start: 0.9034 (ptt90) cc_final: 0.8548 (ptt-90) REVERT: D 626 MET cc_start: 0.7890 (tpp) cc_final: 0.7625 (tpp) REVERT: D 647 GLU cc_start: 0.9136 (pp20) cc_final: 0.8917 (pp20) REVERT: E 95 MET cc_start: 0.9223 (ppp) cc_final: 0.8927 (ppp) REVERT: E 340 ASN cc_start: 0.8911 (p0) cc_final: 0.8370 (m-40) REVERT: E 373 MET cc_start: 0.9137 (ttp) cc_final: 0.8160 (tmm) REVERT: E 381 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 35 TRP cc_start: 0.8829 (m100) cc_final: 0.8456 (m100) REVERT: A 381 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8114 (tp30) REVERT: A 454 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9253 (mm) REVERT: F 522 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.6283 (t80) REVERT: F 530 MET cc_start: 0.8689 (mmm) cc_final: 0.8299 (mmm) REVERT: F 579 ARG cc_start: 0.9298 (mtp85) cc_final: 0.8868 (mtm-85) REVERT: F 589 ASP cc_start: 0.8743 (m-30) cc_final: 0.8458 (m-30) REVERT: F 601 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7602 (ptpp) REVERT: F 621 MET cc_start: 0.8571 (tpp) cc_final: 0.8268 (tpp) REVERT: F 629 MET cc_start: 0.9309 (mmm) cc_final: 0.8819 (tpt) REVERT: F 647 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8251 (mt-10) REVERT: F 655 LYS cc_start: 0.8753 (ptpp) cc_final: 0.8467 (ptpp) outliers start: 52 outliers final: 46 residues processed: 228 average time/residue: 0.1187 time to fit residues: 41.9304 Evaluate side-chains 236 residues out of total 1628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 614 TRP Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 469 ARG Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 554 ASN Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 HIS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 564 HIS Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 627 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 103 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 175 optimal weight: 0.0470 chunk 135 optimal weight: 2.9990 chunk 71 optimal weight: 0.1980 chunk 127 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 overall best weight: 0.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** D 575 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 = 0.3615 r_free = 0.3615 target = 0.083470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.063258 restraints weight = 61655.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.065372 restraints weight = 33621.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.066751 restraints weight = 23734.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.067600 restraints weight = 19323.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.068116 restraints weight = 17116.113| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18270 Z= 0.143 Angle : 0.836 11.057 25247 Z= 0.368 Chirality : 0.047 0.389 3514 Planarity : 0.004 0.040 2724 Dihedral : 10.062 116.448 6975 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.17 % Favored : 93.72 % Rotamer: Outliers : 3.13 % Allowed : 23.77 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.19), residues: 1814 helix: 0.26 (0.24), residues: 453 sheet: -0.49 (0.26), residues: 391 loop : -1.06 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 327 TYR 0.028 0.001 TYR B 586 PHE 0.025 0.001 PHE A 383 TRP 0.073 0.002 TRP C 400 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (17994) covalent geometry : angle 0.76748 / 0.35 (24449) SS BOND : bond 0.00375 / 0.26 ( 30) SS BOND : angle 1.33378 / 0.79 ( 60) hydrogen bonds : bond 0.04170 / 2.85 ( 516) hydrogen bonds : angle 5.26256 / 3.81 ( 1551) link_ALPHA1-2 : bond 0.00802 / 0.41 ( 6) link_ALPHA1-2 : angle 2.51730 / 1.53 ( 18) link_ALPHA1-3 : bond 0.01783 / 0.93 ( 17) link_ALPHA1-3 : angle 2.94796 / 1.77 ( 51) link_ALPHA1-6 : bond 0.00722 / 0.43 ( 16) link_ALPHA1-6 : angle 1.55630 / 0.95 ( 48) link_BETA1-4 : bond 0.00712 / 0.50 ( 122) link_BETA1-4 : angle 2.22593 / 1.66 ( 366) link_BETA1-6 : bond 0.00552 / 0.28 ( 12) link_BETA1-6 : angle 1.45257 / 0.85 ( 36) link_NAG-ASN : bond 0.00223 / 0.15 ( 73) link_NAG-ASN : angle 1.61507 / 1.18 ( 219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2634.17 seconds wall clock time: 46 minutes 52.17 seconds (2812.17 seconds total)