Starting phenix.real_space_refine on Sat Jun 28 11:59:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b4h_43892/06_2025/9b4h_43892.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b4h_43892/06_2025/9b4h_43892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b4h_43892/06_2025/9b4h_43892.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b4h_43892/06_2025/9b4h_43892.map" model { file = "/net/cci-nas-00/data/ceres_data/9b4h_43892/06_2025/9b4h_43892.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b4h_43892/06_2025/9b4h_43892.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.054 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 163 5.16 5 C 20037 2.51 5 N 4652 2.21 5 O 7476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32328 Number of models: 1 Model: "" Number of chains: 110 Chain: "A" Number of atoms: 13867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1908, 13867 Classifications: {'peptide': 1908} Link IDs: {'PCIS': 11, 'PTRANS': 136, 'TRANS': 1760} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 114 Planarities with less than four sites: {'HYP:plan-1': 57} Unresolved non-hydrogen planarities: 57 Chain: "X" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 834 Classifications: {'peptide': 109} Link IDs: {'TRANS': 108} Chain breaks: 5 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 166 Planarities with less than four sites: {'HYP:plan-1': 83} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 13867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1908, 13867 Classifications: {'peptide': 1908} Link IDs: {'PCIS': 11, 'PTRANS': 136, 'TRANS': 1760} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 114 Planarities with less than four sites: {'HYP:plan-1': 57} Unresolved non-hydrogen planarities: 57 Chain: "A1" 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: "A2" 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: "A3" 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: "A4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "A5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "A6" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "A7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "A9" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "B0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "B1" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "B3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "B4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "B5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "B6" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "B7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "B9" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C1" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C2" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C6" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C8" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "C9" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D1" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D2" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D6" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D8" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "D9" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "E0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "E1" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "E2" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "E4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "E5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "E6" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 72 Unusual residues: {'FUB': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E8" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "F0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "F3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "F6" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "F7" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "F8" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "a1" 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: "a2" 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: "a3" 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: "a4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'34V': 1, 'FUB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "a5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "a6" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "a7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "a9" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "b0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "b1" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "b3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "b4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "b5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "b6" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "b7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "b9" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c1" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c2" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c6" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c8" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "c9" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d1" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d2" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e1" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e2" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e4" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e8" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e9" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 54 Unusual residues: {'FUB': 6} 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: "f0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "f3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "f5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "f6" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "f7" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {'FUB': 4} 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: "f8" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "E3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "f2" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e6" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "e3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d9" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d8" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d6" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "d0" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "F5" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "F2" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: "E7" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'FUB': 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: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 770 Unusual residues: {'A1AIO': 57, 'GLA': 13} Classifications: {'undetermined': 70} Link IDs: {None: 69} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 70 Chain: "B" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 770 Unusual residues: {'A1AIO': 57, 'GLA': 13} Classifications: {'undetermined': 70} Link IDs: {None: 69} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 70 Time building chain proxies: 22.00, per 1000 atoms: 0.68 Number of scatterers: 32328 At special positions: 0 Unit cell: (116.76, 122.32, 593.53, 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 163 16.00 O 7476 8.00 N 4652 7.00 C 20037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 594 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 790 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 905 " - pdb=" SG CYS A 947 " distance=2.03 Simple disulfide: pdb=" SG CYS A1182 " - pdb=" SG CYS A1213 " distance=2.03 Simple disulfide: pdb=" SG CYS A1216 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1247 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1287 " - pdb=" SG CYS A1301 " distance=2.03 Simple disulfide: pdb=" SG CYS A1304 " - pdb=" SG CYS A1317 " distance=2.03 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1358 " distance=2.03 Simple disulfide: pdb=" SG CYS A1361 " - pdb=" SG CYS A1389 " distance=2.03 Simple disulfide: pdb=" SG CYS A1392 " - pdb=" SG CYS A1405 " distance=2.03 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1445 " distance=2.03 Simple disulfide: pdb=" SG CYS A1448 " - pdb=" SG CYS A1462 " distance=2.03 Simple disulfide: pdb=" SG CYS A1465 " - pdb=" SG CYS A1479 " distance=2.03 Simple disulfide: pdb=" SG CYS A1596 " - pdb=" SG CYS A1610 " distance=2.03 Simple disulfide: pdb=" SG CYS A1613 " - pdb=" SG CYS A1627 " distance=2.03 Simple disulfide: pdb=" SG CYS A1666 " - pdb=" SG CYS A1680 " distance=2.03 Simple disulfide: pdb=" SG CYS A1683 " - pdb=" SG CYS A1697 " distance=2.03 Simple disulfide: pdb=" SG CYS A1700 " - pdb=" SG CYS A1714 " distance=2.03 Simple disulfide: pdb=" SG CYS A1733 " - pdb=" SG CYS A1747 " distance=2.04 Simple disulfide: pdb=" SG CYS A1750 " - pdb=" SG CYS A1765 " distance=2.03 Simple disulfide: pdb=" SG CYS A1768 " - pdb=" SG CYS A1794 " distance=2.03 Simple disulfide: pdb=" SG CYS A1797 " - pdb=" SG CYS A1811 " distance=2.03 Simple disulfide: pdb=" SG CYS A1814 " - pdb=" SG CYS A1837 " distance=2.03 Simple disulfide: pdb=" SG CYS A1828 " - pdb=" SG CYS A1840 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 594 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 790 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 905 " - pdb=" SG CYS B 947 " distance=2.03 Simple disulfide: pdb=" SG CYS B1182 " - pdb=" SG CYS B1213 " distance=2.03 Simple disulfide: pdb=" SG CYS B1216 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1231 " - pdb=" SG CYS B1244 " distance=2.03 Simple disulfide: pdb=" SG CYS B1247 " - pdb=" SG CYS B1284 " distance=2.03 Simple disulfide: pdb=" SG CYS B1287 " - pdb=" SG CYS B1301 " distance=2.03 Simple disulfide: pdb=" SG CYS B1304 " - pdb=" SG CYS B1317 " distance=2.03 Simple disulfide: pdb=" SG CYS B1320 " - pdb=" SG CYS B1358 " distance=2.03 Simple disulfide: pdb=" SG CYS B1361 " - pdb=" SG CYS B1389 " distance=2.03 Simple disulfide: pdb=" SG CYS B1392 " - pdb=" SG CYS B1405 " distance=2.03 Simple disulfide: pdb=" SG CYS B1408 " - pdb=" SG CYS B1445 " distance=2.03 Simple disulfide: pdb=" SG CYS B1448 " - pdb=" SG CYS B1462 " distance=2.03 Simple disulfide: pdb=" SG CYS B1465 " - pdb=" SG CYS B1479 " distance=2.04 Simple disulfide: pdb=" SG CYS B1596 " - pdb=" SG CYS B1610 " distance=2.03 Simple disulfide: pdb=" SG CYS B1613 " - pdb=" SG CYS B1627 " distance=2.03 Simple disulfide: pdb=" SG CYS B1666 " - pdb=" SG CYS B1680 " distance=2.03 Simple disulfide: pdb=" SG CYS B1683 " - pdb=" SG CYS B1697 " distance=2.03 Simple disulfide: pdb=" SG CYS B1700 " - pdb=" SG CYS B1714 " distance=2.03 Simple disulfide: pdb=" SG CYS B1733 " - pdb=" SG CYS B1747 " distance=2.04 Simple disulfide: pdb=" SG CYS B1750 " - pdb=" SG CYS B1765 " distance=2.03 Simple disulfide: pdb=" SG CYS B1768 " - pdb=" SG CYS B1794 " distance=2.03 Simple disulfide: pdb=" SG CYS B1797 " - pdb=" SG CYS B1811 " distance=2.03 Simple disulfide: pdb=" SG CYS B1814 " - pdb=" SG CYS B1837 " distance=2.03 Simple disulfide: pdb=" SG CYS B1828 " - pdb=" SG CYS B1840 " 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=243, symmetry=0 Links applied ALPHA1-2 " FUBA4 1 " - " FUBA4 2 " ~> Even though FUB is a beta isomer, an alpha linkage is required... " FUBA5 1 " - " FUBA5 2 " " FUBA6 1 " - " FUBA6 2 " " FUBA6 3 " - " FUBA6 4 " " FUBA7 1 " - " FUBA7 2 " " FUBA9 1 " - " FUBA9 2 " " FUBA9 3 " - " FUBA9 4 " " FUBB0 1 " - " FUBB0 2 " " FUBB1 1 " - " FUBB1 2 " " FUBB3 1 " - " FUBB3 2 " " FUBB4 1 " - " FUBB4 2 " " FUBB5 1 " - " FUBB5 2 " " FUBB6 1 " - " FUBB6 2 " " FUBB6 3 " - " FUBB6 4 " " FUBB7 1 " - " FUBB7 2 " " FUBB9 1 " - " FUBB9 2 " " FUBC0 1 " - " FUBC0 2 " " FUBC1 1 " - " FUBC1 2 " " FUBC2 1 " - " FUBC2 2 " " FUBC3 1 " - " FUBC3 2 " " FUBC4 1 " - " FUBC4 2 " " FUBC5 1 " - " FUBC5 2 " " FUBC6 1 " - " FUBC6 2 " " FUBC7 1 " - " FUBC7 2 " " FUBC8 1 " - " FUBC8 2 " " FUBC9 1 " - " FUBC9 2 " " FUBD0 1 " - " FUBD0 2 " " FUBD1 1 " - " FUBD1 2 " " FUBD2 1 " - " FUBD2 2 " " FUBD3 1 " - " FUBD3 2 " " FUBD4 1 " - " FUBD4 2 " " FUBD5 1 " - " FUBD5 2 " " FUBD6 1 " - " FUBD6 2 " " FUBD7 1 " - " FUBD7 2 " " FUBD8 1 " - " FUBD8 2 " " FUBD9 1 " - " FUBD9 2 " " FUBE0 1 " - " FUBE0 2 " " FUBE1 1 " - " FUBE1 2 " " FUBE2 1 " - " FUBE2 2 " " FUBE3 1 " - " FUBE3 2 " " FUBE4 1 " - " FUBE4 2 " " FUBE5 1 " - " FUBE5 2 " " FUBE6 1 " - " FUBE6 2 " " FUBE6 3 " - " FUBE6 4 " " FUBE6 5 " - " FUBE6 6 " " FUBE6 7 " - " FUBE6 8 " " FUBE7 1 " - " FUBE7 2 " " FUBE8 1 " - " FUBE8 2 " " FUBF0 1 " - " FUBF0 2 " " FUBF2 1 " - " FUBF2 2 " " FUBF3 1 " - " FUBF3 2 " " FUBF5 1 " - " FUBF5 2 " " FUBF6 1 " - " FUBF6 2 " " FUBF6 3 " - " FUBF6 4 " " FUBF7 1 " - " FUBF7 2 " " FUBF7 3 " - " FUBF7 4 " " FUBF8 1 " - " FUBF8 2 " " FUBa5 1 " - " FUBa5 2 " " FUBa6 1 " - " FUBa6 2 " " FUBa6 3 " - " FUBa6 4 " " FUBa7 1 " - " FUBa7 2 " " FUBa9 1 " - " FUBa9 2 " " FUBa9 3 " - " FUBa9 4 " " FUBb0 1 " - " FUBb0 2 " " FUBb1 1 " - " FUBb1 2 " " FUBb3 1 " - " FUBb3 2 " " FUBb4 1 " - " FUBb4 2 " " FUBb5 1 " - " FUBb5 2 " " FUBb6 1 " - " FUBb6 2 " " FUBb6 3 " - " FUBb6 4 " " FUBb7 1 " - " FUBb7 2 " " FUBb9 1 " - " FUBb9 2 " " FUBc0 1 " - " FUBc0 2 " " FUBc1 1 " - " FUBc1 2 " " FUBc2 1 " - " FUBc2 2 " " FUBc3 1 " - " FUBc3 2 " " FUBc4 1 " - " FUBc4 2 " " FUBc5 1 " - " FUBc5 2 " " FUBc6 1 " - " FUBc6 2 " " FUBc7 1 " - " FUBc7 2 " " FUBc8 1 " - " FUBc8 2 " " FUBc9 1 " - " FUBc9 2 " " FUBd0 1 " - " FUBd0 2 " " FUBd1 1 " - " FUBd1 2 " " FUBd2 1 " - " FUBd2 2 " " FUBd3 1 " - " FUBd3 2 " " FUBd4 1 " - " FUBd4 2 " " FUBd5 1 " - " FUBd5 2 " " FUBd6 1 " - " FUBd6 2 " " FUBd7 1 " - " FUBd7 2 " " FUBd8 1 " - " FUBd8 2 " " FUBd9 1 " - " FUBd9 2 " " FUBe0 1 " - " FUBe0 2 " " FUBe1 1 " - " FUBe1 2 " " FUBe2 1 " - " FUBe2 2 " " FUBe3 1 " - " FUBe3 2 " " FUBe4 1 " - " FUBe4 2 " " FUBe5 1 " - " FUBe5 2 " " FUBe6 1 " - " FUBe6 2 " " FUBe7 1 " - " FUBe7 2 " " FUBe8 1 " - " FUBe8 2 " " FUBe9 1 " - " FUBe9 2 " " FUBe9 3 " - " FUBe9 4 " " FUBe9 5 " - " FUBe9 6 " " FUBf0 1 " - " FUBf0 2 " " FUBf2 1 " - " FUBf2 2 " " FUBf3 1 " - " FUBf3 2 " " FUBf5 1 " - " FUBf5 2 " " FUBf6 1 " - " FUBf6 2 " " FUBf6 3 " - " FUBf6 4 " " FUBf7 1 " - " FUBf7 2 " " FUBf7 3 " - " FUBf7 4 " " FUBf8 1 " - " FUBf8 2 " ALPHA1-4 " 34Va4 1 " - " FUBa4 2 " BETA1-4 " NAGA1 1 " - " NAGA1 2 " " NAGA2 1 " - " NAGA2 2 " " NAGA3 1 " - " NAGA3 2 " " NAGa1 1 " - " NAGa1 2 " " NAGa2 1 " - " NAGa2 2 " " NAGa3 1 " - " NAGa3 2 " NAG-ASN " NAGA1 1 " - " ASN A 851 " " NAGA2 1 " - " ASN A1194 " " NAGA3 1 " - " ASN A1643 " " NAGa1 1 " - " ASN B 851 " " NAGa2 1 " - " ASN B1194 " " NAGa3 1 " - " ASN B1643 " Number of additional bonds: simple=243, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.51 Conformation dependent library (CDL) restraints added in 4.1 seconds 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7234 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 116 sheets defined 3.0% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.91 Creating SS restraints... Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.073A pdb=" N ALA A 260 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 673 through 682 removed outlier: 3.654A pdb=" N GLY A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'A' and resid 1070 through 1076 removed outlier: 3.585A pdb=" N TYR A1074 " --> pdb=" O THR A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1282 No H-bonds generated for 'chain 'A' and resid 1280 through 1282' Processing helix chain 'A' and resid 1424 through 1428 removed outlier: 3.793A pdb=" N ILE A1427 " --> pdb=" O SER A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1497 Processing helix chain 'A' and resid 1846 through 1850 Processing helix chain 'B' and resid 256 through 260 removed outlier: 4.120A pdb=" N ALA B 260 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 673 through 683 removed outlier: 3.892A pdb=" N SER B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 922 removed outlier: 3.532A pdb=" N TRP B 922 " --> pdb=" O ALA B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1076 removed outlier: 3.609A pdb=" N TYR B1074 " --> pdb=" O THR B1070 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B1076 " --> pdb=" O ALA B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1280 through 1282 No H-bonds generated for 'chain 'B' and resid 1280 through 1282' Processing helix chain 'B' and resid 1492 through 1498 Processing helix chain 'B' and resid 1846 through 1850 removed outlier: 3.748A pdb=" N ARG B1850 " --> pdb=" O LYS B1847 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 53 removed outlier: 6.875A pdb=" N THR A 65 " --> pdb=" O LEU A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 209 Processing sheet with id=AA6, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.797A pdb=" N VAL A 261 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 272 removed outlier: 3.545A pdb=" N THR A 339 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 279 through 280 removed outlier: 4.084A pdb=" N ALA A 372 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 286 through 288 Processing sheet with id=AB1, first strand: chain 'A' and resid 385 through 391 removed outlier: 4.341A pdb=" N ALA A 407 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 385 through 391 Processing sheet with id=AB3, first strand: chain 'A' and resid 397 through 398 removed outlier: 6.646A pdb=" N VAL A 397 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 495 through 501 removed outlier: 4.059A pdb=" N VAL A 510 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR A 581 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 560 through 565 Processing sheet with id=AB6, first strand: chain 'A' and resid 560 through 565 Processing sheet with id=AB7, first strand: chain 'A' and resid 620 through 627 Processing sheet with id=AB8, first strand: chain 'A' and resid 630 through 632 Processing sheet with id=AB9, first strand: chain 'A' and resid 686 through 691 Processing sheet with id=AC1, first strand: chain 'A' and resid 751 through 758 Processing sheet with id=AC2, first strand: chain 'A' and resid 804 through 808 removed outlier: 7.128A pdb=" N THR A 835 " --> pdb=" O PRO A 793 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AC4, first strand: chain 'A' and resid 864 through 871 Processing sheet with id=AC5, first strand: chain 'A' and resid 876 through 877 removed outlier: 6.602A pdb=" N VAL A 876 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A1001 " --> pdb=" O GLY A 959 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY A 959 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 933 through 938 Processing sheet with id=AC7, first strand: chain 'A' and resid 1006 through 1014 removed outlier: 5.749A pdb=" N VAL A1008 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A1035 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A1010 " --> pdb=" O THR A1033 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1094 through 1101 removed outlier: 4.370A pdb=" N GLN A1049 " --> pdb=" O TYR A1131 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL A1128 " --> pdb=" O ASN A1139 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A1139 " --> pdb=" O VAL A1128 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU A1130 " --> pdb=" O GLY A1137 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1094 through 1101 removed outlier: 4.370A pdb=" N GLN A1049 " --> pdb=" O TYR A1131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1121 through 1122 Processing sheet with id=AD2, first strand: chain 'A' and resid 1186 through 1191 Processing sheet with id=AD3, first strand: chain 'A' and resid 1194 through 1196 removed outlier: 3.878A pdb=" N ALA A1202 " --> pdb=" O ASN A1194 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR A1196 " --> pdb=" O ARG A1200 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG A1200 " --> pdb=" O THR A1196 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1220 through 1221 Processing sheet with id=AD5, first strand: chain 'A' and resid 1235 through 1236 Processing sheet with id=AD6, first strand: chain 'A' and resid 1251 through 1253 Processing sheet with id=AD7, first strand: chain 'A' and resid 1256 through 1257 Processing sheet with id=AD8, first strand: chain 'A' and resid 1291 through 1292 Processing sheet with id=AD9, first strand: chain 'A' and resid 1308 through 1309 Processing sheet with id=AE1, first strand: chain 'A' and resid 1324 through 1327 Processing sheet with id=AE2, first strand: chain 'A' and resid 1365 through 1366 Processing sheet with id=AE3, first strand: chain 'A' and resid 1396 through 1397 Processing sheet with id=AE4, first strand: chain 'A' and resid 1412 through 1413 Processing sheet with id=AE5, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AE6, first strand: chain 'A' and resid 1452 through 1453 Processing sheet with id=AE7, first strand: chain 'A' and resid 1469 through 1470 removed outlier: 3.557A pdb=" N GLN A1480 " --> pdb=" O PHE A1470 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 1486 through 1487 removed outlier: 3.671A pdb=" N SER A1547 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 1518 through 1519 Processing sheet with id=AF1, first strand: chain 'A' and resid 1553 through 1554 Processing sheet with id=AF2, first strand: chain 'A' and resid 1570 through 1571 Processing sheet with id=AF3, first strand: chain 'A' and resid 1600 through 1601 Processing sheet with id=AF4, first strand: chain 'A' and resid 1617 through 1618 Processing sheet with id=AF5, first strand: chain 'A' and resid 1634 through 1635 Processing sheet with id=AF6, first strand: chain 'A' and resid 1645 through 1647 removed outlier: 3.638A pdb=" N ILE A1652 " --> pdb=" O ASN A1647 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 1670 through 1671 Processing sheet with id=AF8, first strand: chain 'A' and resid 1687 through 1688 Processing sheet with id=AF9, first strand: chain 'A' and resid 1704 through 1705 Processing sheet with id=AG1, first strand: chain 'A' and resid 1721 through 1722 Processing sheet with id=AG2, first strand: chain 'A' and resid 1737 through 1738 Processing sheet with id=AG3, first strand: chain 'A' and resid 1765 through 1767 removed outlier: 4.128A pdb=" N ALA A1779 " --> pdb=" O PHE A1754 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 1772 through 1773 Processing sheet with id=AG5, first strand: chain 'A' and resid 1801 through 1802 Processing sheet with id=AG6, first strand: chain 'A' and resid 1817 through 1820 removed outlier: 6.511A pdb=" N ASN A1823 " --> pdb=" O LEU A1819 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 46 through 53 removed outlier: 5.277A pdb=" N LEU B 47 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA B 71 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU B 49 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR B 69 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYS B 51 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N THR B 67 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.692A pdb=" N GLY B 123 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR B 150 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS B 125 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 127 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR B 146 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 129 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER B 144 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU B 131 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 156 through 162 Processing sheet with id=AH1, first strand: chain 'B' and resid 207 through 209 removed outlier: 3.975A pdb=" N MET B 189 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 232 through 233 removed outlier: 3.697A pdb=" N GLY B 232 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 263 " --> pdb=" O GLY B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'B' and resid 269 through 272 Processing sheet with id=AH4, first strand: chain 'B' and resid 275 through 276 Processing sheet with id=AH5, first strand: chain 'B' and resid 279 through 280 removed outlier: 3.873A pdb=" N ALA B 372 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 385 through 391 removed outlier: 4.517A pdb=" N ALA B 407 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 385 through 391 Processing sheet with id=AH8, first strand: chain 'B' and resid 433 through 435 Processing sheet with id=AH9, first strand: chain 'B' and resid 495 through 501 Processing sheet with id=AI1, first strand: chain 'B' and resid 561 through 565 Processing sheet with id=AI2, first strand: chain 'B' and resid 561 through 565 Processing sheet with id=AI3, first strand: chain 'B' and resid 620 through 627 Processing sheet with id=AI4, first strand: chain 'B' and resid 630 through 632 removed outlier: 6.867A pdb=" N VAL B 631 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 746 " --> pdb=" O GLY B 710 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'B' and resid 686 through 691 Processing sheet with id=AI6, first strand: chain 'B' and resid 751 through 758 Processing sheet with id=AI7, first strand: chain 'B' and resid 804 through 808 removed outlier: 7.038A pdb=" N THR B 835 " --> pdb=" O PRO B 793 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'B' and resid 864 through 871 Processing sheet with id=AI9, first strand: chain 'B' and resid 876 through 877 removed outlier: 6.739A pdb=" N VAL B 876 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL B1001 " --> pdb=" O GLY B 959 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLY B 959 " --> pdb=" O VAL B1001 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'B' and resid 933 through 938 Processing sheet with id=AJ2, first strand: chain 'B' and resid 1006 through 1014 removed outlier: 6.728A pdb=" N THR B1033 " --> pdb=" O GLU B1009 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR B1011 " --> pdb=" O THR B1031 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B1031 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE B1013 " --> pdb=" O TYR B1029 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR B1029 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'B' and resid 1016 through 1018 removed outlier: 8.014A pdb=" N ASN B1016 " --> pdb=" O TYR B1023 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR B1023 " --> pdb=" O ASN B1016 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B1156 " --> pdb=" O PRO B1022 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'B' and resid 1094 through 1101 removed outlier: 4.189A pdb=" N GLN B1049 " --> pdb=" O TYR B1131 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL B1128 " --> pdb=" O ASN B1139 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN B1139 " --> pdb=" O VAL B1128 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLU B1130 " --> pdb=" O GLY B1137 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'B' and resid 1094 through 1101 removed outlier: 4.189A pdb=" N GLN B1049 " --> pdb=" O TYR B1131 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'B' and resid 1121 through 1122 Processing sheet with id=AJ7, first strand: chain 'B' and resid 1186 through 1191 Processing sheet with id=AJ8, first strand: chain 'B' and resid 1194 through 1196 removed outlier: 3.837A pdb=" N ALA B1202 " --> pdb=" O ASN B1194 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR B1196 " --> pdb=" O ARG B1200 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG B1200 " --> pdb=" O THR B1196 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'B' and resid 1235 through 1236 Processing sheet with id=AK1, first strand: chain 'B' and resid 1251 through 1253 Processing sheet with id=AK2, first strand: chain 'B' and resid 1256 through 1257 Processing sheet with id=AK3, first strand: chain 'B' and resid 1291 through 1292 Processing sheet with id=AK4, first strand: chain 'B' and resid 1308 through 1309 Processing sheet with id=AK5, first strand: chain 'B' and resid 1324 through 1327 Processing sheet with id=AK6, first strand: chain 'B' and resid 1365 through 1366 Processing sheet with id=AK7, first strand: chain 'B' and resid 1396 through 1397 Processing sheet with id=AK8, first strand: chain 'B' and resid 1412 through 1413 Processing sheet with id=AK9, first strand: chain 'B' and resid 1421 through 1422 Processing sheet with id=AL1, first strand: chain 'B' and resid 1452 through 1453 Processing sheet with id=AL2, first strand: chain 'B' and resid 1469 through 1470 Processing sheet with id=AL3, first strand: chain 'B' and resid 1518 through 1519 Processing sheet with id=AL4, first strand: chain 'B' and resid 1553 through 1554 Processing sheet with id=AL5, first strand: chain 'B' and resid 1570 through 1571 Processing sheet with id=AL6, first strand: chain 'B' and resid 1600 through 1601 Processing sheet with id=AL7, first strand: chain 'B' and resid 1617 through 1618 Processing sheet with id=AL8, first strand: chain 'B' and resid 1634 through 1635 Processing sheet with id=AL9, first strand: chain 'B' and resid 1645 through 1647 removed outlier: 3.629A pdb=" N ILE B1652 " --> pdb=" O ASN B1647 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'B' and resid 1670 through 1671 Processing sheet with id=AM2, first strand: chain 'B' and resid 1704 through 1705 Processing sheet with id=AM3, first strand: chain 'B' and resid 1721 through 1722 Processing sheet with id=AM4, first strand: chain 'B' and resid 1737 through 1738 Processing sheet with id=AM5, first strand: chain 'B' and resid 1765 through 1767 removed outlier: 4.126A pdb=" N ALA B1779 " --> pdb=" O PHE B1754 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'B' and resid 1772 through 1773 Processing sheet with id=AM7, first strand: chain 'B' and resid 1801 through 1802 Processing sheet with id=AM8, first strand: chain 'B' and resid 1817 through 1818 768 hydrogen bonds defined for protein. 1812 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: 21.04 Time building geometry restraints manager: 15.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9321 1.34 - 1.46: 8313 1.46 - 1.58: 15132 1.58 - 1.70: 226 1.70 - 1.82: 202 Bond restraints: 33194 Sorted by residual: bond pdb=" C04 A1AIO A2043 " pdb=" C05 A1AIO A2043 " ideal model delta sigma weight residual 1.517 1.280 0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C04 A1AIO B2039 " pdb=" C05 A1AIO B2039 " ideal model delta sigma weight residual 1.517 1.280 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C04 A1AIO A2005 " pdb=" C05 A1AIO A2005 " ideal model delta sigma weight residual 1.517 1.280 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C04 A1AIO A2029 " pdb=" C05 A1AIO A2029 " ideal model delta sigma weight residual 1.517 1.281 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C04 A1AIO A2033 " pdb=" C05 A1AIO A2033 " ideal model delta sigma weight residual 1.517 1.281 0.236 2.00e-02 2.50e+03 1.39e+02 ... (remaining 33189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 43329 2.15 - 4.31: 1644 4.31 - 6.46: 464 6.46 - 8.62: 223 8.62 - 10.77: 3 Bond angle restraints: 45663 Sorted by residual: angle pdb=" C ASN B1643 " pdb=" CA ASN B1643 " pdb=" CB ASN B1643 " ideal model delta sigma weight residual 109.37 100.17 9.20 1.91e+00 2.74e-01 2.32e+01 angle pdb=" N ALA B1641 " pdb=" CA ALA B1641 " pdb=" C ALA B1641 " ideal model delta sigma weight residual 108.52 116.79 -8.27 1.74e+00 3.30e-01 2.26e+01 angle pdb=" N ASN B1643 " pdb=" CA ASN B1643 " pdb=" C ASN B1643 " ideal model delta sigma weight residual 109.40 101.76 7.64 1.63e+00 3.76e-01 2.19e+01 angle pdb=" C ALA B1849 " pdb=" N ARG B1850 " pdb=" CA ARG B1850 " ideal model delta sigma weight residual 123.05 116.90 6.15 1.40e+00 5.10e-01 1.93e+01 angle pdb=" N ARG B1850 " pdb=" CA ARG B1850 " pdb=" CB ARG B1850 " ideal model delta sigma weight residual 110.55 103.66 6.89 1.57e+00 4.06e-01 1.93e+01 ... (remaining 45658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 21389 23.14 - 46.27: 1859 46.27 - 69.41: 297 69.41 - 92.54: 54 92.54 - 115.68: 5 Dihedral angle restraints: 23604 sinusoidal: 12303 harmonic: 11301 Sorted by residual: dihedral pdb=" CB CYS B1182 " pdb=" SG CYS B1182 " pdb=" SG CYS B1213 " pdb=" CB CYS B1213 " ideal model delta sinusoidal sigma weight residual 93.00 163.54 -70.54 1 1.00e+01 1.00e-02 6.40e+01 dihedral pdb=" CB CYS A1448 " pdb=" SG CYS A1448 " pdb=" SG CYS A1462 " pdb=" CB CYS A1462 " ideal model delta sinusoidal sigma weight residual -86.00 -154.58 68.58 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A1750 " pdb=" SG CYS A1750 " pdb=" SG CYS A1765 " pdb=" CB CYS A1765 " ideal model delta sinusoidal sigma weight residual -86.00 -153.94 67.94 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 23601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 6376 1.020 - 2.040: 0 2.040 - 3.059: 0 3.059 - 4.079: 0 4.079 - 5.099: 1 Chirality restraints: 6377 Sorted by residual: chirality pdb=" C3 34Va4 1 " pdb=" C2 34Va4 1 " pdb=" C4 34Va4 1 " pdb=" O3 34Va4 1 " both_signs ideal model delta sigma weight residual False 2.47 -2.63 5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" CA ASN B1643 " pdb=" N ASN B1643 " pdb=" C ASN B1643 " pdb=" CB ASN B1643 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" C4 FUBf6 1 " pdb=" C3 FUBf6 1 " pdb=" C5 FUBf6 1 " pdb=" O4 FUBf6 1 " both_signs ideal model delta sigma weight residual False 2.39 2.67 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 6374 not shown) Planarity restraints: 5139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1850 " -0.331 9.50e-02 1.11e+02 1.49e-01 1.35e+01 pdb=" NE ARG B1850 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B1850 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B1850 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B1850 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B1848 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.34e+01 pdb=" C THR B1848 " -0.063 2.00e-02 2.50e+03 pdb=" O THR B1848 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA B1849 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 828 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO A 829 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 829 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 829 " -0.036 5.00e-02 4.00e+02 ... (remaining 5136 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 37 2.19 - 2.87: 12953 2.87 - 3.55: 44638 3.55 - 4.22: 73657 4.22 - 4.90: 122063 Nonbonded interactions: 253348 Sorted by model distance: nonbonded pdb=" OD1 HYP B1921 " pdb=" O4 FUBf2 1 " model vdw 1.517 3.040 nonbonded pdb=" OG1 THR B 944 " pdb=" O5 FUBd9 2 " model vdw 1.614 3.040 nonbonded pdb=" OD1 HYP B1905 " pdb=" O4 FUBd8 1 " model vdw 1.799 3.040 nonbonded pdb=" OD1 HYP B1915 " pdb=" O2 FUBe7 1 " model vdw 1.829 2.432 nonbonded pdb=" OD1 HYP B1911 " pdb=" O2 FUBe3 1 " model vdw 1.947 2.432 ... (remaining 253343 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 'A' selection = chain 'B' } ncs_group { reference = chain 'A1' selection = chain 'A2' selection = chain 'A3' selection = chain 'a1' selection = chain 'a2' selection = chain 'a3' } ncs_group { reference = (chain 'A4' and resid 2) selection = (chain 'A5' and resid 2) selection = (chain 'A7' and resid 2) selection = (chain 'B0' and resid 2) selection = (chain 'B1' and resid 2) selection = (chain 'B3' and resid 2) selection = (chain 'B4' and resid 2) selection = (chain 'B5' and resid 2) selection = (chain 'B7' and resid 2) selection = (chain 'B9' and resid 2) selection = (chain 'C0' and resid 2) selection = (chain 'C1' and resid 2) selection = (chain 'C2' and resid 2) selection = (chain 'C3' and resid 2) selection = (chain 'C4' and resid 2) selection = (chain 'C5' and resid 2) selection = (chain 'C6' and resid 2) selection = (chain 'C7' and resid 2) selection = (chain 'C8' and resid 2) selection = (chain 'C9' and resid 2) selection = (chain 'D0' and resid 2) selection = (chain 'D1' and resid 2) selection = (chain 'D2' and resid 2) selection = (chain 'D3' and resid 2) selection = (chain 'D4' and resid 2) selection = (chain 'D5' and resid 2) selection = (chain 'D6' and resid 2) selection = (chain 'D7' and resid 2) selection = (chain 'D8' and resid 2) selection = (chain 'D9' and resid 2) selection = (chain 'E0' and resid 2) selection = (chain 'E1' and resid 2) selection = (chain 'E2' and resid 2) selection = (chain 'E3' and resid 2) selection = (chain 'E4' and resid 2) selection = (chain 'E5' and resid 2) selection = (chain 'E7' and resid 2) selection = (chain 'E8' and resid 2) selection = (chain 'F0' and resid 2) selection = (chain 'F2' and resid 2) selection = (chain 'F3' and resid 2) selection = (chain 'F5' and resid 2) selection = (chain 'F8' and resid 2) selection = (chain 'a4' and resid 2) selection = (chain 'a5' and resid 2) selection = (chain 'a7' and resid 2) selection = (chain 'b0' and resid 2) selection = (chain 'b1' and resid 2) selection = (chain 'b3' and resid 2) selection = (chain 'b4' and resid 2) selection = (chain 'b5' and resid 2) selection = (chain 'b7' and resid 2) selection = (chain 'b9' and resid 2) selection = (chain 'c0' and resid 2) selection = (chain 'c1' and resid 2) selection = (chain 'c2' and resid 2) selection = (chain 'c3' and resid 2) selection = (chain 'c4' and resid 2) selection = (chain 'c5' and resid 2) selection = (chain 'c6' and resid 2) selection = (chain 'c7' and resid 2) selection = (chain 'c8' and resid 2) selection = (chain 'c9' and resid 2) selection = (chain 'd0' and resid 2) selection = (chain 'd1' and resid 2) selection = (chain 'd2' and resid 2) selection = (chain 'd3' and resid 2) selection = (chain 'd4' and resid 2) selection = (chain 'd5' and resid 2) selection = (chain 'd6' and resid 2) selection = (chain 'd7' and resid 2) selection = (chain 'd8' and resid 2) selection = (chain 'd9' and resid 2) selection = (chain 'e0' and resid 2) selection = (chain 'e1' and resid 2) selection = (chain 'e2' and resid 2) selection = (chain 'e3' and resid 2) selection = (chain 'e4' and resid 2) selection = (chain 'e5' and resid 2) selection = (chain 'e6' and resid 2) selection = (chain 'e7' and resid 2) selection = (chain 'e8' and resid 2) selection = (chain 'f0' and resid 2) selection = (chain 'f2' and resid 2) selection = (chain 'f3' and resid 2) selection = (chain 'f5' and resid 2) selection = (chain 'f8' and resid 2) } ncs_group { reference = chain 'A6' selection = chain 'A9' selection = chain 'B6' selection = chain 'F6' selection = chain 'F7' selection = chain 'a6' selection = chain 'a9' selection = chain 'b6' selection = chain 'f6' selection = chain 'f7' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.320 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 95.180 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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 : 0.020 0.566 33617 Z= 1.134 Angle : 1.033 16.225 46149 Z= 0.399 Chirality : 0.091 5.099 6377 Planarity : 0.004 0.149 5133 Dihedral : 15.887 115.680 16208 Min Nonbonded Distance : 1.517 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.29 % Allowed : 24.84 % Favored : 71.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3654 helix: -0.14 (0.53), residues: 113 sheet: 0.22 (0.15), residues: 1076 loop : -0.12 (0.13), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1397 HIS 0.004 0.001 HIS A1326 PHE 0.013 0.001 PHE B1308 TYR 0.008 0.001 TYR B1325 ARG 0.002 0.000 ARG B1909 Details of bonding type rmsd link_NAG-ASN : bond 0.02164 ( 6) link_NAG-ASN : angle 4.83974 ( 18) link_ALPHA1-4 : bond 0.00184 ( 1) link_ALPHA1-4 : angle 1.18408 ( 3) link_BETA1-4 : bond 0.00742 ( 6) link_BETA1-4 : angle 1.69144 ( 18) link_ALPHA1-2 : bond 0.00478 ( 113) link_ALPHA1-2 : angle 1.22744 ( 339) hydrogen bonds : bond 0.13181 ( 702) hydrogen bonds : angle 5.98231 ( 1812) SS BOND : bond 0.00176 ( 54) SS BOND : angle 1.07679 ( 108) covalent geometry : bond 0.01958 (33194) covalent geometry : angle 1.02707 (45663) Misc. bond : bond 0.06862 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 52 time to evaluate : 3.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8842 (pt0) REVERT: A 1563 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8736 (pt0) REVERT: A 1621 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.9068 (mtpt) REVERT: A 1715 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8782 (mtmt) REVERT: A 1945 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7046 (pm20) REVERT: B 211 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6848 (mp) REVERT: B 1170 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8054 (mm-40) REVERT: B 1853 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8411 (pm20) REVERT: B 1945 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7610 (pm20) outliers start: 96 outliers final: 71 residues processed: 144 average time/residue: 0.3894 time to fit residues: 96.7628 Evaluate side-chains 126 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 46 time to evaluate : 2.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1342 ASP Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1534 ASP Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1621 LYS Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1748 THR Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1943 VAL Chi-restraints excluded: chain A residue 1945 GLN Chi-restraints excluded: chain X residue 1492 THR Chi-restraints excluded: chain X residue 1561 THR Chi-restraints excluded: chain X residue 1624 ASP Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1081 THR Chi-restraints excluded: chain B residue 1134 SER Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1170 GLN Chi-restraints excluded: chain B residue 1277 LEU Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1534 ASP Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1591 THR Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1654 THR Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1800 ASP Chi-restraints excluded: chain B residue 1808 VAL Chi-restraints excluded: chain B residue 1840 CYS Chi-restraints excluded: chain B residue 1853 GLN Chi-restraints excluded: chain B residue 1861 SER Chi-restraints excluded: chain B residue 1876 ASN Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 157 optimal weight: 0.1980 chunk 305 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 354 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.047625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.038866 restraints weight = 165721.567| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.99 r_work: 0.2734 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 33617 Z= 0.309 Angle : 0.776 9.835 46149 Z= 0.349 Chirality : 0.051 0.269 6377 Planarity : 0.004 0.067 5133 Dihedral : 10.140 81.269 10835 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.62 % Allowed : 22.82 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3654 helix: -0.30 (0.53), residues: 116 sheet: 0.16 (0.16), residues: 1024 loop : -0.28 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 771 HIS 0.005 0.002 HIS A 411 PHE 0.019 0.002 PHE B1308 TYR 0.014 0.002 TYR A 921 ARG 0.006 0.001 ARG A1881 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 6) link_NAG-ASN : angle 3.30071 ( 18) link_ALPHA1-4 : bond 0.00639 ( 1) link_ALPHA1-4 : angle 3.08108 ( 3) link_BETA1-4 : bond 0.00427 ( 6) link_BETA1-4 : angle 2.15406 ( 18) link_ALPHA1-2 : bond 0.00407 ( 113) link_ALPHA1-2 : angle 1.73409 ( 339) hydrogen bonds : bond 0.03117 ( 702) hydrogen bonds : angle 5.23621 ( 1812) SS BOND : bond 0.00319 ( 54) SS BOND : angle 1.41905 ( 108) covalent geometry : bond 0.00683 (33194) covalent geometry : angle 0.75768 (45663) Misc. bond : bond 0.00138 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 48 time to evaluate : 4.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9189 (mm) REVERT: A 928 ILE cc_start: 0.8440 (pp) cc_final: 0.8228 (mm) REVERT: A 1563 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8849 (pt0) REVERT: A 1621 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9000 (mtpt) REVERT: A 1622 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.6935 (mtt180) REVERT: A 1658 LYS cc_start: 0.9524 (OUTLIER) cc_final: 0.8877 (ttmm) REVERT: A 1715 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8547 (mtpp) REVERT: A 1729 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9413 (mt) REVERT: A 1746 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8240 (pm20) REVERT: A 1809 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8683 (ttm110) REVERT: B 211 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7151 (mp) REVERT: B 1170 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7987 (mm-40) REVERT: B 1176 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9118 (ttpp) REVERT: B 1261 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8543 (mtp180) REVERT: B 1853 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8451 (pm20) REVERT: B 1945 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7592 (pm20) outliers start: 164 outliers final: 108 residues processed: 207 average time/residue: 0.4363 time to fit residues: 162.1129 Evaluate side-chains 171 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 48 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1059 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1405 CYS Chi-restraints excluded: chain A residue 1416 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1621 LYS Chi-restraints excluded: chain A residue 1622 ARG Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1658 LYS Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1729 LEU Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1746 GLN Chi-restraints excluded: chain A residue 1748 THR Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1943 VAL Chi-restraints excluded: chain X residue 1492 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain B residue 1148 THR Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1170 GLN Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1261 ARG Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1441 LEU Chi-restraints excluded: chain B residue 1497 MET Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1808 VAL Chi-restraints excluded: chain B residue 1848 THR Chi-restraints excluded: chain B residue 1853 GLN Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1943 VAL Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 155 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 365 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.048082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.039252 restraints weight = 165267.135| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.14 r_work: 0.2745 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33617 Z= 0.199 Angle : 0.654 9.580 46149 Z= 0.302 Chirality : 0.047 0.276 6377 Planarity : 0.004 0.070 5133 Dihedral : 7.817 87.701 10783 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 5.10 % Allowed : 23.54 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3654 helix: -0.24 (0.53), residues: 116 sheet: 0.11 (0.16), residues: 990 loop : -0.25 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1397 HIS 0.005 0.001 HIS A 411 PHE 0.015 0.001 PHE B1308 TYR 0.010 0.001 TYR B1208 ARG 0.004 0.000 ARG A1881 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 6) link_NAG-ASN : angle 3.19955 ( 18) link_ALPHA1-4 : bond 0.00321 ( 1) link_ALPHA1-4 : angle 2.73900 ( 3) link_BETA1-4 : bond 0.00386 ( 6) link_BETA1-4 : angle 1.82990 ( 18) link_ALPHA1-2 : bond 0.00278 ( 113) link_ALPHA1-2 : angle 1.40693 ( 339) hydrogen bonds : bond 0.02914 ( 702) hydrogen bonds : angle 5.03469 ( 1812) SS BOND : bond 0.00260 ( 54) SS BOND : angle 1.18966 ( 108) covalent geometry : bond 0.00444 (33194) covalent geometry : angle 0.63888 (45663) Misc. bond : bond 0.00095 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 49 time to evaluate : 3.980 Fit side-chains revert: symmetry clash REVERT: A 887 THR cc_start: 0.9549 (OUTLIER) cc_final: 0.9088 (p) REVERT: A 1239 GLU cc_start: 0.9058 (mp0) cc_final: 0.8842 (pm20) REVERT: A 1537 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.5910 (t80) REVERT: A 1563 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8837 (pt0) REVERT: A 1621 LYS cc_start: 0.9459 (OUTLIER) cc_final: 0.9045 (mtpt) REVERT: A 1622 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7067 (mtt180) REVERT: A 1658 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9071 (ttmt) REVERT: A 1715 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8615 (mtpp) REVERT: A 1729 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9402 (mt) REVERT: A 1809 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8684 (ttm110) REVERT: A 1945 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: B 211 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7158 (mp) REVERT: B 1170 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8020 (mm-40) REVERT: B 1176 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9113 (ttpp) REVERT: B 1261 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8431 (mtp180) REVERT: B 1394 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8505 (t0) REVERT: B 1945 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7644 (pm20) outliers start: 149 outliers final: 97 residues processed: 193 average time/residue: 0.3659 time to fit residues: 125.4308 Evaluate side-chains 160 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 47 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1416 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1537 PHE Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1621 LYS Chi-restraints excluded: chain A residue 1622 ARG Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1658 LYS Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1729 LEU Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1748 THR Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1945 GLN Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain B residue 1148 THR Chi-restraints excluded: chain B residue 1170 GLN Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1261 ARG Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1394 ASP Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1441 LEU Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1591 THR Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1654 THR Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1709 ILE Chi-restraints excluded: chain B residue 1848 THR Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 330 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 343 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 93 optimal weight: 0.0370 chunk 157 optimal weight: 3.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.047263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.038411 restraints weight = 167468.822| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.11 r_work: 0.2716 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 33617 Z= 0.329 Angle : 0.763 9.589 46149 Z= 0.348 Chirality : 0.050 0.267 6377 Planarity : 0.004 0.065 5133 Dihedral : 8.174 86.831 10771 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 6.92 % Allowed : 21.93 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3654 helix: -0.39 (0.53), residues: 116 sheet: 0.02 (0.16), residues: 1033 loop : -0.40 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1397 HIS 0.006 0.002 HIS A 411 PHE 0.021 0.002 PHE B1308 TYR 0.014 0.002 TYR B 952 ARG 0.006 0.000 ARG A1493 Details of bonding type rmsd link_NAG-ASN : bond 0.00746 ( 6) link_NAG-ASN : angle 3.25165 ( 18) link_ALPHA1-4 : bond 0.00269 ( 1) link_ALPHA1-4 : angle 2.37224 ( 3) link_BETA1-4 : bond 0.00443 ( 6) link_BETA1-4 : angle 2.42860 ( 18) link_ALPHA1-2 : bond 0.00419 ( 113) link_ALPHA1-2 : angle 1.67820 ( 339) hydrogen bonds : bond 0.03138 ( 702) hydrogen bonds : angle 5.18700 ( 1812) SS BOND : bond 0.00349 ( 54) SS BOND : angle 1.42502 ( 108) covalent geometry : bond 0.00724 (33194) covalent geometry : angle 0.74512 (45663) Misc. bond : bond 0.00140 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 50 time to evaluate : 3.108 Fit side-chains revert: symmetry clash REVERT: A 142 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9160 (mm) REVERT: A 589 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8419 (tp40) REVERT: A 612 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8724 (tp40) REVERT: A 887 THR cc_start: 0.9564 (OUTLIER) cc_final: 0.9121 (p) REVERT: A 1239 GLU cc_start: 0.9093 (mp0) cc_final: 0.8869 (pm20) REVERT: A 1537 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.5886 (t80) REVERT: A 1563 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8810 (pt0) REVERT: A 1621 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.8994 (mtpt) REVERT: A 1622 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.6926 (mtt180) REVERT: A 1658 LYS cc_start: 0.9543 (OUTLIER) cc_final: 0.8886 (ttmm) REVERT: A 1715 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8444 (mtpp) REVERT: A 1809 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8710 (ttm110) REVERT: X 1600 MET cc_start: 0.7240 (ppp) cc_final: 0.6971 (ppp) REVERT: B 211 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7340 (mp) REVERT: B 608 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8366 (p) REVERT: B 1170 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7902 (mm-40) REVERT: B 1176 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9136 (ttpp) REVERT: B 1261 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.8611 (mtp180) REVERT: B 1729 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9231 (mm) REVERT: B 1766 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8529 (mtm-85) REVERT: B 1853 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8642 (pm20) REVERT: B 1945 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7555 (pm20) outliers start: 202 outliers final: 134 residues processed: 243 average time/residue: 0.3785 time to fit residues: 160.7739 Evaluate side-chains 202 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 48 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 997 THR Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1033 THR Chi-restraints excluded: chain A residue 1059 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1416 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1537 PHE Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1621 LYS Chi-restraints excluded: chain A residue 1622 ARG Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1658 LYS Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1943 VAL Chi-restraints excluded: chain X residue 1492 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1026 ILE Chi-restraints excluded: chain B residue 1031 THR Chi-restraints excluded: chain B residue 1059 ASN Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1078 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1170 GLN Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1223 MET Chi-restraints excluded: chain B residue 1261 ARG Chi-restraints excluded: chain B residue 1277 LEU Chi-restraints excluded: chain B residue 1330 VAL Chi-restraints excluded: chain B residue 1339 THR Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1379 ASN Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1441 LEU Chi-restraints excluded: chain B residue 1482 CYS Chi-restraints excluded: chain B residue 1497 MET Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1591 THR Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1654 THR Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1729 LEU Chi-restraints excluded: chain B residue 1766 ARG Chi-restraints excluded: chain B residue 1808 VAL Chi-restraints excluded: chain B residue 1840 CYS Chi-restraints excluded: chain B residue 1848 THR Chi-restraints excluded: chain B residue 1853 GLN Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 65 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 chunk 365 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 352 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.048022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.039167 restraints weight = 163816.021| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.20 r_work: 0.2740 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33617 Z= 0.179 Angle : 0.645 9.792 46149 Z= 0.299 Chirality : 0.047 0.274 6377 Planarity : 0.004 0.068 5133 Dihedral : 7.136 81.184 10770 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.48 % Allowed : 23.06 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.14), residues: 3654 helix: -0.31 (0.53), residues: 116 sheet: 0.04 (0.16), residues: 1023 loop : -0.32 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1397 HIS 0.004 0.001 HIS A 411 PHE 0.017 0.001 PHE B1308 TYR 0.010 0.001 TYR B1208 ARG 0.002 0.000 ARG B1881 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 6) link_NAG-ASN : angle 3.18016 ( 18) link_ALPHA1-4 : bond 0.00213 ( 1) link_ALPHA1-4 : angle 2.25016 ( 3) link_BETA1-4 : bond 0.00360 ( 6) link_BETA1-4 : angle 1.95821 ( 18) link_ALPHA1-2 : bond 0.00302 ( 113) link_ALPHA1-2 : angle 1.33565 ( 339) hydrogen bonds : bond 0.02705 ( 702) hydrogen bonds : angle 5.00580 ( 1812) SS BOND : bond 0.00233 ( 54) SS BOND : angle 1.18521 ( 108) covalent geometry : bond 0.00397 (33194) covalent geometry : angle 0.63060 (45663) Misc. bond : bond 0.00088 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 49 time to evaluate : 4.960 Fit side-chains revert: symmetry clash REVERT: A 589 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8499 (tp-100) REVERT: A 612 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8687 (tp40) REVERT: A 887 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9048 (p) REVERT: A 1075 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.8985 (ttmm) REVERT: A 1239 GLU cc_start: 0.9185 (mp0) cc_final: 0.8921 (pm20) REVERT: A 1537 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.5844 (t80) REVERT: A 1563 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8768 (pt0) REVERT: A 1621 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.8991 (mtpt) REVERT: A 1622 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7009 (mtt180) REVERT: A 1658 LYS cc_start: 0.9518 (OUTLIER) cc_final: 0.9050 (ttmt) REVERT: A 1715 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8504 (mtpp) REVERT: A 1728 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8417 (pp20) REVERT: A 1809 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8654 (ttm110) REVERT: X 1600 MET cc_start: 0.7175 (ppp) cc_final: 0.6915 (ppp) REVERT: B 211 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7423 (mt) REVERT: B 1170 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7880 (mm-40) REVERT: B 1176 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9117 (ttpp) REVERT: B 1261 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8401 (mtp180) REVERT: B 1853 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8624 (pm20) REVERT: B 1945 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7482 (pm20) outliers start: 160 outliers final: 114 residues processed: 204 average time/residue: 0.5663 time to fit residues: 206.2989 Evaluate side-chains 180 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 48 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1059 ASN Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1416 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1515 THR Chi-restraints excluded: chain A residue 1537 PHE Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1621 LYS Chi-restraints excluded: chain A residue 1622 ARG Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1658 LYS Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1728 GLU Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1943 VAL Chi-restraints excluded: chain X residue 1492 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1170 GLN Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1261 ARG Chi-restraints excluded: chain B residue 1277 LEU Chi-restraints excluded: chain B residue 1312 SER Chi-restraints excluded: chain B residue 1340 SER Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1441 LEU Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1591 THR Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1709 ILE Chi-restraints excluded: chain B residue 1808 VAL Chi-restraints excluded: chain B residue 1840 CYS Chi-restraints excluded: chain B residue 1848 THR Chi-restraints excluded: chain B residue 1853 GLN Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 70 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 151 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.047532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.038760 restraints weight = 165552.007| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.05 r_work: 0.2724 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 33617 Z= 0.276 Angle : 0.710 9.553 46149 Z= 0.325 Chirality : 0.049 0.277 6377 Planarity : 0.004 0.062 5133 Dihedral : 7.484 80.402 10769 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 6.13 % Allowed : 22.58 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.14), residues: 3654 helix: -0.38 (0.53), residues: 116 sheet: -0.00 (0.16), residues: 1024 loop : -0.39 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1397 HIS 0.006 0.002 HIS A 411 PHE 0.019 0.002 PHE B1308 TYR 0.012 0.001 TYR B 952 ARG 0.004 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00670 ( 6) link_NAG-ASN : angle 3.17559 ( 18) link_ALPHA1-4 : bond 0.00120 ( 1) link_ALPHA1-4 : angle 2.25303 ( 3) link_BETA1-4 : bond 0.00383 ( 6) link_BETA1-4 : angle 2.26874 ( 18) link_ALPHA1-2 : bond 0.00357 ( 113) link_ALPHA1-2 : angle 1.54769 ( 339) hydrogen bonds : bond 0.02929 ( 702) hydrogen bonds : angle 5.06702 ( 1812) SS BOND : bond 0.00299 ( 54) SS BOND : angle 1.32666 ( 108) covalent geometry : bond 0.00611 (33194) covalent geometry : angle 0.69356 (45663) Misc. bond : bond 0.00121 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 49 time to evaluate : 3.049 Fit side-chains revert: symmetry clash REVERT: A 218 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8657 (t0) REVERT: A 589 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8410 (tp40) REVERT: A 612 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8706 (tp40) REVERT: A 1075 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.8999 (ttmm) REVERT: A 1405 CYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6470 (m) REVERT: A 1537 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.5860 (t80) REVERT: A 1563 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8787 (pt0) REVERT: A 1621 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.8996 (mtpt) REVERT: A 1622 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.6902 (mtt180) REVERT: A 1658 LYS cc_start: 0.9520 (OUTLIER) cc_final: 0.8892 (ttmm) REVERT: A 1715 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8426 (mtpp) REVERT: A 1728 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8443 (pp20) REVERT: A 1809 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8690 (ttm110) REVERT: X 1600 MET cc_start: 0.7222 (ppp) cc_final: 0.6939 (ppp) REVERT: B 211 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7644 (mt) REVERT: B 942 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: B 1170 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7832 (mm-40) REVERT: B 1176 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9127 (ttpp) REVERT: B 1261 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8512 (mtp180) REVERT: B 1322 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8544 (mm-30) REVERT: B 1853 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8686 (pm20) REVERT: B 1945 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7589 (pm20) outliers start: 179 outliers final: 130 residues processed: 221 average time/residue: 0.3574 time to fit residues: 138.0710 Evaluate side-chains 200 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 49 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 892 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1059 ASN Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1405 CYS Chi-restraints excluded: chain A residue 1416 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1515 THR Chi-restraints excluded: chain A residue 1537 PHE Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1588 VAL Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1621 LYS Chi-restraints excluded: chain A residue 1622 ARG Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1658 LYS Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1728 GLU Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1943 VAL Chi-restraints excluded: chain X residue 1492 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1059 ASN Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1170 GLN Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1223 MET Chi-restraints excluded: chain B residue 1261 ARG Chi-restraints excluded: chain B residue 1277 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain B residue 1340 SER Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1379 ASN Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1428 THR Chi-restraints excluded: chain B residue 1441 LEU Chi-restraints excluded: chain B residue 1459 MET Chi-restraints excluded: chain B residue 1482 CYS Chi-restraints excluded: chain B residue 1497 MET Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1591 THR Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1654 THR Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1709 ILE Chi-restraints excluded: chain B residue 1808 VAL Chi-restraints excluded: chain B residue 1848 THR Chi-restraints excluded: chain B residue 1853 GLN Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 352 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 220 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 233 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.048166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.039370 restraints weight = 163917.575| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.14 r_work: 0.2750 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 33617 Z= 0.162 Angle : 0.635 9.923 46149 Z= 0.295 Chirality : 0.047 0.274 6377 Planarity : 0.004 0.064 5133 Dihedral : 6.763 78.043 10765 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.62 % Allowed : 23.23 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3654 helix: -0.32 (0.53), residues: 116 sheet: 0.03 (0.16), residues: 1019 loop : -0.30 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1397 HIS 0.004 0.001 HIS A 411 PHE 0.016 0.001 PHE B1308 TYR 0.009 0.001 TYR B1795 ARG 0.002 0.000 ARG A1493 Details of bonding type rmsd link_NAG-ASN : bond 0.00664 ( 6) link_NAG-ASN : angle 3.17465 ( 18) link_ALPHA1-4 : bond 0.00177 ( 1) link_ALPHA1-4 : angle 2.03705 ( 3) link_BETA1-4 : bond 0.00379 ( 6) link_BETA1-4 : angle 1.92540 ( 18) link_ALPHA1-2 : bond 0.00288 ( 113) link_ALPHA1-2 : angle 1.29254 ( 339) hydrogen bonds : bond 0.02618 ( 702) hydrogen bonds : angle 4.93761 ( 1812) SS BOND : bond 0.00217 ( 54) SS BOND : angle 1.24230 ( 108) covalent geometry : bond 0.00361 (33194) covalent geometry : angle 0.62104 (45663) Misc. bond : bond 0.00084 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 49 time to evaluate : 3.142 Fit side-chains revert: symmetry clash REVERT: A 218 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8660 (t0) REVERT: A 589 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8371 (tp40) REVERT: A 612 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8696 (tp40) REVERT: A 887 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9035 (p) REVERT: A 1075 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.8984 (ttmm) REVERT: A 1537 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.5845 (t80) REVERT: A 1563 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8768 (pt0) REVERT: A 1621 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.8985 (mtpt) REVERT: A 1658 LYS cc_start: 0.9512 (OUTLIER) cc_final: 0.9027 (ttmt) REVERT: A 1715 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8501 (mtpp) REVERT: A 1728 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8440 (pp20) REVERT: A 1809 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8660 (ttm110) REVERT: A 1945 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: X 1600 MET cc_start: 0.7187 (ppp) cc_final: 0.6899 (ppp) REVERT: B 211 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7413 (mt) REVERT: B 942 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: B 1170 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7829 (mm-40) REVERT: B 1176 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9106 (ttpp) REVERT: B 1261 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8460 (mtp180) REVERT: B 1322 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8525 (mm-30) REVERT: B 1853 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8674 (pm20) REVERT: B 1945 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7484 (pm20) outliers start: 164 outliers final: 122 residues processed: 208 average time/residue: 0.3839 time to fit residues: 142.4055 Evaluate side-chains 192 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 49 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1059 ASN Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1416 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1515 THR Chi-restraints excluded: chain A residue 1537 PHE Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1621 LYS Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1658 LYS Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1698 LYS Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1728 GLU Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1943 VAL Chi-restraints excluded: chain A residue 1945 GLN Chi-restraints excluded: chain X residue 1492 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1147 VAL Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1170 GLN Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1261 ARG Chi-restraints excluded: chain B residue 1277 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain B residue 1340 SER Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1441 LEU Chi-restraints excluded: chain B residue 1459 MET Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1591 THR Chi-restraints excluded: chain B residue 1598 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1654 THR Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1808 VAL Chi-restraints excluded: chain B residue 1848 THR Chi-restraints excluded: chain B residue 1853 GLN Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 289 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 378 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 166 optimal weight: 0.9980 chunk 321 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.048479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.039707 restraints weight = 162828.155| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.15 r_work: 0.2762 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33617 Z= 0.140 Angle : 0.613 9.997 46149 Z= 0.285 Chirality : 0.046 0.275 6377 Planarity : 0.004 0.061 5133 Dihedral : 6.211 77.482 10765 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.14 % Allowed : 23.60 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3654 helix: -0.34 (0.53), residues: 116 sheet: 0.08 (0.16), residues: 1019 loop : -0.23 (0.13), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1397 HIS 0.004 0.001 HIS A1326 PHE 0.014 0.001 PHE B1308 TYR 0.008 0.001 TYR A 832 ARG 0.002 0.000 ARG B1622 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 6) link_NAG-ASN : angle 3.14761 ( 18) link_ALPHA1-4 : bond 0.00273 ( 1) link_ALPHA1-4 : angle 1.87385 ( 3) link_BETA1-4 : bond 0.00412 ( 6) link_BETA1-4 : angle 1.79577 ( 18) link_ALPHA1-2 : bond 0.00300 ( 113) link_ALPHA1-2 : angle 1.22273 ( 339) hydrogen bonds : bond 0.02478 ( 702) hydrogen bonds : angle 4.77909 ( 1812) SS BOND : bond 0.00205 ( 54) SS BOND : angle 1.15457 ( 108) covalent geometry : bond 0.00315 (33194) covalent geometry : angle 0.60021 (45663) Misc. bond : bond 0.00075 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 48 time to evaluate : 3.021 Fit side-chains revert: symmetry clash REVERT: A 589 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8633 (tp-100) REVERT: A 887 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9009 (p) REVERT: A 1537 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.5835 (t80) REVERT: A 1563 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8741 (pt0) REVERT: A 1658 LYS cc_start: 0.9510 (OUTLIER) cc_final: 0.8963 (ttmt) REVERT: A 1715 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8539 (mtpp) REVERT: A 1728 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8441 (pp20) REVERT: A 1809 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8645 (ttm110) REVERT: A 1945 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.6882 (pm20) REVERT: X 1600 MET cc_start: 0.7164 (ppp) cc_final: 0.6871 (ppp) REVERT: B 942 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8224 (mp0) REVERT: B 1170 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8006 (mm-40) REVERT: B 1176 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9108 (ttpp) REVERT: B 1261 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8347 (mtp180) REVERT: B 1322 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8509 (mm-30) REVERT: B 1853 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: B 1945 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.7454 (pm20) outliers start: 150 outliers final: 115 residues processed: 194 average time/residue: 0.3521 time to fit residues: 120.4305 Evaluate side-chains 179 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 48 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1059 ASN Chi-restraints excluded: chain A residue 1110 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1416 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1537 PHE Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1658 LYS Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1728 GLU Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1945 GLN Chi-restraints excluded: chain X residue 1492 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1170 GLN Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1261 ARG Chi-restraints excluded: chain B residue 1277 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain B residue 1340 SER Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1441 LEU Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1591 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1654 THR Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1709 ILE Chi-restraints excluded: chain B residue 1808 VAL Chi-restraints excluded: chain B residue 1848 THR Chi-restraints excluded: chain B residue 1853 GLN Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 381 optimal weight: 6.9990 chunk 330 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 356 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 328 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 305 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.047774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.039042 restraints weight = 165578.021| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.01 r_work: 0.2743 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 33617 Z= 0.250 Angle : 0.689 11.246 46149 Z= 0.316 Chirality : 0.048 0.271 6377 Planarity : 0.004 0.064 5133 Dihedral : 6.728 78.824 10758 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.04 % Allowed : 23.64 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3654 helix: -0.32 (0.53), residues: 116 sheet: -0.01 (0.16), residues: 1039 loop : -0.30 (0.13), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1397 HIS 0.005 0.001 HIS A 411 PHE 0.017 0.001 PHE B1308 TYR 0.011 0.001 TYR B 952 ARG 0.004 0.000 ARG A1493 Details of bonding type rmsd link_NAG-ASN : bond 0.00695 ( 6) link_NAG-ASN : angle 3.14601 ( 18) link_ALPHA1-4 : bond 0.00066 ( 1) link_ALPHA1-4 : angle 2.08523 ( 3) link_BETA1-4 : bond 0.00393 ( 6) link_BETA1-4 : angle 2.21873 ( 18) link_ALPHA1-2 : bond 0.00314 ( 113) link_ALPHA1-2 : angle 1.46526 ( 339) hydrogen bonds : bond 0.02810 ( 702) hydrogen bonds : angle 4.92877 ( 1812) SS BOND : bond 0.00278 ( 54) SS BOND : angle 1.28866 ( 108) covalent geometry : bond 0.00553 (33194) covalent geometry : angle 0.67351 (45663) Misc. bond : bond 0.00111 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 48 time to evaluate : 2.971 Fit side-chains revert: symmetry clash REVERT: A 218 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8653 (t0) REVERT: A 589 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8413 (tp40) REVERT: A 1537 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.5855 (t80) REVERT: A 1563 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8775 (pt0) REVERT: A 1622 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.6980 (mtt180) REVERT: A 1658 LYS cc_start: 0.9530 (OUTLIER) cc_final: 0.8843 (ttmm) REVERT: A 1715 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8544 (mtpp) REVERT: A 1728 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8457 (pp20) REVERT: A 1809 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8680 (ttm110) REVERT: A 1945 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: X 1600 MET cc_start: 0.7000 (ppp) cc_final: 0.6719 (ppp) REVERT: B 942 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: B 1170 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.7988 (mm-40) REVERT: B 1176 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9118 (ttpp) REVERT: B 1261 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8456 (mtp180) REVERT: B 1322 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8560 (mm-30) REVERT: B 1853 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: B 1945 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7470 (pm20) outliers start: 147 outliers final: 124 residues processed: 191 average time/residue: 0.3734 time to fit residues: 127.0487 Evaluate side-chains 189 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 48 time to evaluate : 2.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1059 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1182 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1416 THR Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1537 PHE Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1622 ARG Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1658 LYS Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1678 THR Chi-restraints excluded: chain A residue 1708 SER Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1728 GLU Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1943 VAL Chi-restraints excluded: chain A residue 1945 GLN Chi-restraints excluded: chain X residue 1492 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1170 GLN Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1261 ARG Chi-restraints excluded: chain B residue 1277 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain B residue 1340 SER Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1441 LEU Chi-restraints excluded: chain B residue 1459 MET Chi-restraints excluded: chain B residue 1482 CYS Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1591 THR Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1654 THR Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1709 ILE Chi-restraints excluded: chain B residue 1808 VAL Chi-restraints excluded: chain B residue 1848 THR Chi-restraints excluded: chain B residue 1853 GLN Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 176 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 319 optimal weight: 4.9990 chunk 375 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.048596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.039820 restraints weight = 162539.019| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.15 r_work: 0.2765 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33617 Z= 0.122 Angle : 0.606 11.026 46149 Z= 0.283 Chirality : 0.046 0.278 6377 Planarity : 0.004 0.061 5133 Dihedral : 6.012 77.500 10758 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.15 % Allowed : 24.63 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3654 helix: -0.27 (0.53), residues: 116 sheet: 0.05 (0.16), residues: 1033 loop : -0.22 (0.13), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1397 HIS 0.005 0.001 HIS A1326 PHE 0.014 0.001 PHE B1308 TYR 0.008 0.001 TYR A 262 ARG 0.002 0.000 ARG A1390 Details of bonding type rmsd link_NAG-ASN : bond 0.00650 ( 6) link_NAG-ASN : angle 3.18049 ( 18) link_ALPHA1-4 : bond 0.00335 ( 1) link_ALPHA1-4 : angle 1.82419 ( 3) link_BETA1-4 : bond 0.00430 ( 6) link_BETA1-4 : angle 1.74120 ( 18) link_ALPHA1-2 : bond 0.00323 ( 113) link_ALPHA1-2 : angle 1.16830 ( 339) hydrogen bonds : bond 0.02466 ( 702) hydrogen bonds : angle 4.77582 ( 1812) SS BOND : bond 0.00195 ( 54) SS BOND : angle 1.09306 ( 108) covalent geometry : bond 0.00275 (33194) covalent geometry : angle 0.59446 (45663) Misc. bond : bond 0.00067 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7308 Ramachandran restraints generated. 3654 Oldfield, 0 Emsley, 3654 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 49 time to evaluate : 3.147 Fit side-chains revert: symmetry clash REVERT: A 218 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8660 (t0) REVERT: A 589 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8450 (tp40) REVERT: A 1537 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.5864 (t80) REVERT: A 1658 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.8951 (ttmt) REVERT: A 1715 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8620 (mtpp) REVERT: A 1728 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8470 (pp20) REVERT: A 1809 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8640 (ttm110) REVERT: A 1945 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.6889 (pm20) REVERT: X 1600 MET cc_start: 0.6806 (ppp) cc_final: 0.6532 (ppp) REVERT: B 437 MET cc_start: 0.8946 (mmm) cc_final: 0.8685 (mmm) REVERT: B 608 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8360 (p) REVERT: B 942 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: B 1176 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9105 (ttpp) REVERT: B 1261 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8369 (mtp180) REVERT: B 1322 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8491 (mm-30) REVERT: B 1853 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8677 (pm20) REVERT: B 1945 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7390 (pm20) outliers start: 121 outliers final: 99 residues processed: 165 average time/residue: 0.3537 time to fit residues: 103.8554 Evaluate side-chains 162 residues out of total 2919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 48 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 541 THR Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 589 GLN Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 790 CYS Chi-restraints excluded: chain A residue 791 GLN Chi-restraints excluded: chain A residue 833 PHE Chi-restraints excluded: chain A residue 835 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1059 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1182 CYS Chi-restraints excluded: chain A residue 1203 VAL Chi-restraints excluded: chain A residue 1296 ILE Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1332 THR Chi-restraints excluded: chain A residue 1357 THR Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1380 LEU Chi-restraints excluded: chain A residue 1434 VAL Chi-restraints excluded: chain A residue 1493 ARG Chi-restraints excluded: chain A residue 1500 VAL Chi-restraints excluded: chain A residue 1537 PHE Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1638 VAL Chi-restraints excluded: chain A residue 1658 LYS Chi-restraints excluded: chain A residue 1677 THR Chi-restraints excluded: chain A residue 1715 LYS Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain A residue 1728 GLU Chi-restraints excluded: chain A residue 1744 SER Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1843 LEU Chi-restraints excluded: chain A residue 1895 THR Chi-restraints excluded: chain A residue 1945 GLN Chi-restraints excluded: chain X residue 1492 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 386 THR Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 660 CYS Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 790 CYS Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 942 GLU Chi-restraints excluded: chain B residue 967 VAL Chi-restraints excluded: chain B residue 979 THR Chi-restraints excluded: chain B residue 1011 THR Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1020 THR Chi-restraints excluded: chain B residue 1070 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1176 LYS Chi-restraints excluded: chain B residue 1261 ARG Chi-restraints excluded: chain B residue 1277 LEU Chi-restraints excluded: chain B residue 1322 GLU Chi-restraints excluded: chain B residue 1367 LEU Chi-restraints excluded: chain B residue 1387 THR Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1441 LEU Chi-restraints excluded: chain B residue 1459 MET Chi-restraints excluded: chain B residue 1580 ASN Chi-restraints excluded: chain B residue 1600 THR Chi-restraints excluded: chain B residue 1629 ILE Chi-restraints excluded: chain B residue 1654 THR Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1808 VAL Chi-restraints excluded: chain B residue 1848 THR Chi-restraints excluded: chain B residue 1853 GLN Chi-restraints excluded: chain B residue 1895 THR Chi-restraints excluded: chain B residue 1935 SER Chi-restraints excluded: chain B residue 1945 GLN Chi-restraints excluded: chain B residue 1948 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 320 optimal weight: 4.9990 chunk 116 optimal weight: 0.3980 chunk 266 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 282 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.048202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.039507 restraints weight = 164185.887| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.02 r_work: 0.2757 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33617 Z= 0.187 Angle : 0.639 11.125 46149 Z= 0.295 Chirality : 0.047 0.275 6377 Planarity : 0.004 0.062 5133 Dihedral : 6.190 78.143 10751 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.35 % Allowed : 24.29 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3654 helix: -0.26 (0.53), residues: 116 sheet: 0.01 (0.16), residues: 997 loop : -0.21 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1397 HIS 0.004 0.001 HIS A 411 PHE 0.015 0.001 PHE B1308 TYR 0.010 0.001 TYR B1208 ARG 0.002 0.000 ARG A1493 Details of bonding type rmsd link_NAG-ASN : bond 0.00653 ( 6) link_NAG-ASN : angle 3.15149 ( 18) link_ALPHA1-4 : bond 0.00066 ( 1) link_ALPHA1-4 : angle 1.83436 ( 3) link_BETA1-4 : bond 0.00383 ( 6) link_BETA1-4 : angle 2.02530 ( 18) link_ALPHA1-2 : bond 0.00277 ( 113) link_ALPHA1-2 : angle 1.31984 ( 339) hydrogen bonds : bond 0.02607 ( 702) hydrogen bonds : angle 4.81434 ( 1812) SS BOND : bond 0.00231 ( 54) SS BOND : angle 1.17567 ( 108) covalent geometry : bond 0.00415 (33194) covalent geometry : angle 0.62533 (45663) Misc. bond : bond 0.00091 ( 243) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 15811.45 seconds wall clock time: 276 minutes 15.13 seconds (16575.13 seconds total)