Starting phenix.real_space_refine on Wed May 21 06:38:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvd_27735/05_2025/8dvd_27735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvd_27735/05_2025/8dvd_27735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvd_27735/05_2025/8dvd_27735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvd_27735/05_2025/8dvd_27735.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvd_27735/05_2025/8dvd_27735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvd_27735/05_2025/8dvd_27735.cif" } resolution = 4.12 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= 0.003 sd= 0.056 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 134 5.16 5 C 12814 2.51 5 N 3101 2.21 5 O 4755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20804 Number of models: 1 Model: "" Number of chains: 83 Chain: "A" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1059 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain breaks: 1 Chain: "B" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "C" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1073 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "E" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3962 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "F" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3962 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "G" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3962 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "H" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1102 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 848 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "f" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "r" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "u" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "v" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "z" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "0" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "5" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "8" 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: "9" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "CA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "DA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "EA" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "FA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "GA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "HA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "IA" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "JA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "KA" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "LA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "MA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "NA" 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: "OA" 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: "PA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "QA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "RA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'MAN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.07, per 1000 atoms: 0.63 Number of scatterers: 20804 At special positions: 0 Unit cell: (147.288, 139.707, 162.45, 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 134 16.00 O 4755 8.00 N 3101 7.00 C 12814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS F 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 149E" - pdb=" SG CYS E 149K" distance=2.02 Simple disulfide: pdb=" SG CYS E 183 " - pdb=" SG CYS E 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 149E" - pdb=" SG CYS F 149K" distance=2.03 Simple disulfide: pdb=" SG CYS F 183 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.02 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 149E" - pdb=" SG CYS G 149K" distance=2.03 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 191 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN Y 4 " - " MAN Y 5 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN e 4 " - " MAN e 5 " " MAN f 4 " - " MAN f 5 " " MAN t 4 " - " MAN t 5 " " MAN x 4 " - " MAN x 5 " " MAN z 4 " - " MAN z 5 " " MANEA 4 " - " MANEA 5 " " MANIA 4 " - " MANIA 5 " " MANKA 4 " - " MANKA 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA 4 3 " - " MAN 4 4 " " BMA 5 3 " - " MAN 5 4 " " BMA 7 3 " - " MAN 7 4 " " BMA 9 3 " - " MAN 9 4 " " BMA D 3 " - " MAN D 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " " MAN e 6 " - " MAN e 7 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " BMA o 3 " - " MAN o 4 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 4 " " BMA s 3 " - " MAN s 4 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA x 3 " - " MAN x 4 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " " BMABA 3 " - " MANBA 4 " " BMACA 3 " - " MANCA 4 " " BMADA 3 " - " MANDA 4 " " BMAEA 3 " - " MANEA 4 " " BMAGA 3 " - " MANGA 4 " " BMAIA 3 " - " MANIA 4 " " BMAJA 3 " - " MANJA 4 " " BMAKA 3 " - " MANKA 4 " " MANKA 6 " - " MANKA 7 " " BMALA 3 " - " MANLA 4 " " BMAPA 3 " - " MANPA 4 " " BMAQA 3 " - " MANQA 4 " ALPHA1-6 " BMA 0 3 " - " MAN 0 5 " " BMA 4 3 " - " MAN 4 5 " " BMA 9 3 " - " MAN 9 5 " " BMA M 3 " - " MAN M 5 " " BMA P 3 " - " MAN P 5 " " BMA T 3 " - " MAN T 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 6 " " BMA a 3 " - " MAN a 5 " " BMA c 3 " - " MAN c 7 " " MAN c 7 " - " MAN c 8 " " BMA e 3 " - " MAN e 6 " " MAN e 6 " - " MAN e 8 " " BMA f 3 " - " MAN f 6 " " MAN f 6 " - " MAN f 8 " " BMA j 3 " - " MAN j 5 " " BMA o 3 " - " MAN o 5 " " BMA s 3 " - " MAN s 5 " " BMA t 3 " - " MAN t 6 " " BMA u 3 " - " MAN u 4 " " BMA v 3 " - " MAN v 5 " " BMA x 3 " - " MAN x 6 " " MAN x 6 " - " MAN x 7 " " BMA z 3 " - " MAN z 6 " " BMADA 3 " - " MANDA 5 " " BMAEA 3 " - " MANEA 6 " " BMAFA 3 " - " MANFA 4 " " BMAGA 3 " - " MANGA 5 " " BMAIA 3 " - " MANIA 6 " " MANIA 6 " - " MANIA 7 " " BMAKA 3 " - " MANKA 6 " " MANKA 6 " - " MANKA 8 " " BMALA 3 " - " MANLA 5 " " BMAPA 3 " - " MANPA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 7 2 " - " BMA 7 3 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGFA 2 " - " BMAFA 3 " " NAGGA 1 " - " NAGGA 2 " " NAGGA 2 " - " BMAGA 3 " " NAGHA 1 " - " NAGHA 2 " " NAGHA 2 " - " BMAHA 3 " " NAGIA 1 " - " NAGIA 2 " " NAGIA 2 " - " BMAIA 3 " " NAGJA 1 " - " NAGJA 2 " " NAGJA 2 " - " BMAJA 3 " " NAGKA 1 " - " NAGKA 2 " " NAGKA 2 " - " BMAKA 3 " " NAGLA 1 " - " NAGLA 2 " " NAGLA 2 " - " BMALA 3 " " NAGMA 1 " - " NAGMA 2 " " NAGMA 2 " - " BMAMA 3 " " NAGNA 1 " - " NAGNA 2 " " NAGOA 1 " - " NAGOA 2 " " NAGPA 1 " - " NAGPA 2 " " NAGPA 2 " - " BMAPA 3 " " NAGQA 1 " - " NAGQA 2 " " NAGQA 2 " - " BMAQA 3 " " NAGRA 1 " - " NAGRA 2 " " NAGRA 2 " - " BMARA 3 " NAG-ASN " NAG 0 1 " - " ASN F 160 " " NAG 1 1 " - " ASN F 173 " " NAG 2 1 " - " ASN F 185B" " NAG 3 1 " - " ASN F 354E" " NAG 4 1 " - " ASN F 280 " " NAG 5 1 " - " ASN F 301 " " NAG 6 1 " - " ASN F 468 " " NAG 7 1 " - " ASN G 97 " " NAG 8 1 " - " ASN G 88 " " NAG 9 1 " - " ASN G 132 " " NAG D 1 " - " ASN A 612 " " NAG E 601 " - " ASN E 464 " " NAG F 602 " - " ASN F 464 " " NAG G 601 " - " ASN G 464 " " NAG I 1 " - " ASN A 625 " " NAG J 1 " - " ASN A 641 " " NAG K 1 " - " ASN B 612 " " NAG M 1 " - " ASN B 625 " " NAG N 1 " - " ASN B 641 " " NAG O 1 " - " ASN C 612 " " NAG P 1 " - " ASN C 625 " " NAG Q 1 " - " ASN C 641 " " NAG R 1 " - " ASN E 97 " " NAG S 1 " - " ASN E 88 " " NAG T 1 " - " ASN E 132 " " NAG U 1 " - " ASN E 187 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 229 " " NAG X 1 " - " ASN E 446 " " NAG Y 1 " - " ASN E 360 " " NAG Z 1 " - " ASN E 267A" " NAG a 1 " - " ASN E 291 " " NAG b 1 " - " ASN E 149 " " NAG c 1 " - " ASN E 262 " " NAG d 1 " - " ASN E 149J" " NAG e 1 " - " ASN E 47 " " NAG f 1 " - " ASN E 160 " " NAG g 1 " - " ASN E 301 " " NAG h 1 " - " ASN E 185B" " NAG i 1 " - " ASN E 354E" " NAG j 1 " - " ASN E 280 " " NAG k 1 " - " ASN E 468 " " NAG l 1 " - " ASN E 173 " " NAG m 1 " - " ASN F 97 " " NAG n 1 " - " ASN F 88 " " NAG o 1 " - " ASN F 132 " " NAG p 1 " - " ASN F 187 " " NAG q 1 " - " ASN F 197 " " NAG r 1 " - " ASN F 229 " " NAG s 1 " - " ASN F 446 " " NAG t 1 " - " ASN F 360 " " NAG u 1 " - " ASN F 267A" " NAG v 1 " - " ASN F 291 " " NAG w 1 " - " ASN F 149 " " NAG x 1 " - " ASN F 262 " " NAG y 1 " - " ASN F 149J" " NAG z 1 " - " ASN F 47 " " NAGAA 1 " - " ASN G 187 " " NAGBA 1 " - " ASN G 197 " " NAGCA 1 " - " ASN G 229 " " NAGDA 1 " - " ASN G 446 " " NAGEA 1 " - " ASN G 360 " " NAGFA 1 " - " ASN G 267A" " NAGGA 1 " - " ASN G 291 " " NAGHA 1 " - " ASN G 149 " " NAGIA 1 " - " ASN G 262 " " NAGJA 1 " - " ASN G 149J" " NAGKA 1 " - " ASN G 47 " " NAGLA 1 " - " ASN G 160 " " NAGMA 1 " - " ASN G 173 " " NAGNA 1 " - " ASN G 185B" " NAGOA 1 " - " ASN G 354E" " NAGPA 1 " - " ASN G 280 " " NAGQA 1 " - " ASN G 468 " " NAGRA 1 " - " ASN G 301 " Time building additional restraints: 9.85 Conformation dependent library (CDL) restraints added in 2.1 seconds 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4010 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 32 sheets defined 25.4% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 512 through 522 removed outlier: 3.943A pdb=" N PHE A 522 " --> pdb=" O GLY A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 3.751A pdb=" N GLY A 527 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.570A pdb=" N ILE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 removed outlier: 3.569A pdb=" N ILE A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 664 removed outlier: 4.561A pdb=" N LYS A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASN A 641 " --> pdb=" O PHE A 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.020A pdb=" N THR B 525 " --> pdb=" O PHE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 553 removed outlier: 3.966A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 597 removed outlier: 3.535A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 589 " --> pdb=" O LYS B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 664 removed outlier: 4.493A pdb=" N PHE B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ASN B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 521 Processing helix chain 'C' and resid 522 through 526 removed outlier: 3.744A pdb=" N THR C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 553 removed outlier: 3.728A pdb=" N ALA C 546 " --> pdb=" O ARG C 542 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL C 549 " --> pdb=" O LEU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 597 Processing helix chain 'C' and resid 627 through 637 removed outlier: 3.510A pdb=" N ARG C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS C 634 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 637 " --> pdb=" O ARG C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 664 Processing helix chain 'E' and resid 98 through 117 Processing helix chain 'E' and resid 132 through 139 removed outlier: 4.015A pdb=" N ARG E 138 " --> pdb=" O SER E 134 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TRP E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 149D through 149I removed outlier: 3.613A pdb=" N GLN E 149H" --> pdb=" O SER E 149D" (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 179 No H-bonds generated for 'chain 'E' and resid 177 through 179' Processing helix chain 'E' and resid 338 through 352 removed outlier: 3.958A pdb=" N GLU E 344 " --> pdb=" O ASP E 340 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 396 removed outlier: 3.638A pdb=" N GLU E 395 " --> pdb=" O LEU E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 474 through 477 Processing helix chain 'E' and resid 478 through 483 removed outlier: 3.520A pdb=" N GLU E 482 " --> pdb=" O LEU E 478 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU E 483 " --> pdb=" O TYR E 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 478 through 483' Processing helix chain 'F' and resid 98 through 116 removed outlier: 3.592A pdb=" N SER F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.520A pdb=" N LEU F 125 " --> pdb=" O LEU F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 139 removed outlier: 3.764A pdb=" N TRP F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 149D through 149I removed outlier: 3.647A pdb=" N GLN F 149H" --> pdb=" O SER F 149D" (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 149I" --> pdb=" O CYS F 149E" (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 149D through 149I' Processing helix chain 'F' and resid 287 through 291 removed outlier: 3.880A pdb=" N TYR F 290 " --> pdb=" O ASN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 352 removed outlier: 3.536A pdb=" N LYS F 343 " --> pdb=" O LYS F 339 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU F 344 " --> pdb=" O ASP F 340 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.716A pdb=" N PHE F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 396 removed outlier: 3.556A pdb=" N LEU F 391 " --> pdb=" O MET F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 Processing helix chain 'F' and resid 476 through 484 removed outlier: 3.849A pdb=" N ARG F 480 " --> pdb=" O ALA F 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.616A pdb=" N TRP G 109 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.600A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 139 removed outlier: 3.749A pdb=" N ARG G 138 " --> pdb=" O SER G 134 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 149D through 149I removed outlier: 3.820A pdb=" N GLN G 149H" --> pdb=" O SER G 149D" (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 338 through 352 removed outlier: 3.572A pdb=" N GLU G 344 " --> pdb=" O ASP G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 359 removed outlier: 3.687A pdb=" N ILE G 359 " --> pdb=" O THR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.637A pdb=" N THR G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 395 removed outlier: 3.550A pdb=" N LEU G 391 " --> pdb=" O MET G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 476 No H-bonds generated for 'chain 'G' and resid 474 through 476' Processing helix chain 'G' and resid 477 through 483 removed outlier: 3.620A pdb=" N LEU G 481 " --> pdb=" O GLU G 477 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU G 482 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 483 " --> pdb=" O TYR G 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 477 through 483' Processing helix chain 'H' and resid 26 through 31 removed outlier: 5.834A pdb=" N PHE H 29 " --> pdb=" O GLY H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 9.532A pdb=" N CYS B 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N TYR G 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 603 through 609 removed outlier: 9.376A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.052A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 74 through 76 Processing sheet with id=AA5, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.696A pdb=" N GLU E 174 " --> pdb=" O CYS E 157 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE E 159 " --> pdb=" O TYR E 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.548A pdb=" N VAL E 182 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.894A pdb=" N GLN E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.511A pdb=" N THR E 282 " --> pdb=" O ALA E 454 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 454 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN E 360 " --> pdb=" O ILE E 469 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N MET E 471 " --> pdb=" O ASN E 360 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR E 362 " --> pdb=" O MET E 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 376 through 378 removed outlier: 3.717A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 305 through 308 removed outlier: 3.593A pdb=" N SER E 317 " --> pdb=" O LEU E 305 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AB3, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.876A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AB5, first strand: chain 'F' and resid 129 through 132 removed outlier: 3.993A pdb=" N TYR F 192 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL F 182 " --> pdb=" O TYR F 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'F' and resid 158 through 159 removed outlier: 3.557A pdb=" N PHE F 159 " --> pdb=" O TYR F 172 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.884A pdb=" N GLN F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 424 " --> pdb=" O VAL F 434 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 260 through 261 removed outlier: 6.378A pdb=" N GLY F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN F 360 " --> pdb=" O ILE F 469 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N MET F 471 " --> pdb=" O ASN F 360 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N THR F 362 " --> pdb=" O MET F 471 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 271 through 273 removed outlier: 5.899A pdb=" N GLY F 441 " --> pdb=" O GLY F 300 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY F 300 " --> pdb=" O GLY F 441 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS F 378 " --> pdb=" O GLU F 381 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.759A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'G' and resid 129 through 132 Processing sheet with id=AC5, first strand: chain 'G' and resid 155 through 159 removed outlier: 3.658A pdb=" N CYS G 157 " --> pdb=" O GLU G 174 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.534A pdb=" N GLN G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 256 through 257 removed outlier: 4.063A pdb=" N TRP G 375 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU G 381 " --> pdb=" O CYS G 378 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG G 298 " --> pdb=" O LEU G 443 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLY G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLY G 441 " --> pdb=" O GLY G 300 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA G 454 " --> pdb=" O THR G 282 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.614A pdb=" N GLY G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN G 360 " --> pdb=" O ILE G 469 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 307 through 308 Processing sheet with id=AD1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.801A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP H 50 " --> pdb=" O GLY H 56 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY H 56 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 100 through 100E removed outlier: 6.767A pdb=" N GLU H 100O" --> pdb=" O ASP H 100B" (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE H 100D" --> pdb=" O TYR H 100M" (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR H 100M" --> pdb=" O PHE H 100D" (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.528A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.704A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.34 Time building geometry restraints manager: 10.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2963 1.31 - 1.44: 6629 1.44 - 1.57: 11427 1.57 - 1.70: 3 1.70 - 1.83: 181 Bond restraints: 21203 Sorted by residual: bond pdb=" OH TYS H 100F" pdb=" S TYS H 100F" ideal model delta sigma weight residual 1.679 1.576 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" OH TYS H 100I" pdb=" S TYS H 100I" ideal model delta sigma weight residual 1.679 1.599 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C2 MAN c 5 " pdb=" O2 MAN c 5 " ideal model delta sigma weight residual 1.407 1.471 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" CZ TYS H 100I" pdb=" OH TYS H 100I" ideal model delta sigma weight residual 1.371 1.433 -0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" CZ TYS H 100F" pdb=" OH TYS H 100F" ideal model delta sigma weight residual 1.371 1.428 -0.057 2.00e-02 2.50e+03 8.03e+00 ... (remaining 21198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 27219 2.10 - 4.21: 1088 4.21 - 6.31: 495 6.31 - 8.42: 25 8.42 - 10.52: 1 Bond angle restraints: 28828 Sorted by residual: angle pdb=" CA LEU C 663 " pdb=" C LEU C 663 " pdb=" N ASN C 664 " ideal model delta sigma weight residual 117.07 110.48 6.59 1.14e+00 7.69e-01 3.34e+01 angle pdb=" CA CYS G 205 " pdb=" CB CYS G 205 " pdb=" SG CYS G 205 " ideal model delta sigma weight residual 114.40 124.92 -10.52 2.30e+00 1.89e-01 2.09e+01 angle pdb=" CA LEU C 663 " pdb=" C LEU C 663 " pdb=" O LEU C 663 " ideal model delta sigma weight residual 120.82 125.16 -4.34 1.05e+00 9.07e-01 1.71e+01 angle pdb=" CA LEU A 663 " pdb=" C LEU A 663 " pdb=" N ASN A 664 " ideal model delta sigma weight residual 117.07 112.70 4.37 1.14e+00 7.69e-01 1.47e+01 angle pdb=" N ASN E 149J" pdb=" CA ASN E 149J" pdb=" CB ASN E 149J" ideal model delta sigma weight residual 112.63 107.46 5.17 1.61e+00 3.86e-01 1.03e+01 ... (remaining 28823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 14883 25.15 - 50.30: 822 50.30 - 75.45: 188 75.45 - 100.60: 357 100.60 - 125.76: 225 Dihedral angle restraints: 16475 sinusoidal: 10260 harmonic: 6215 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -162.71 76.71 1 1.00e+01 1.00e-02 7.39e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual 93.00 153.06 -60.06 1 1.00e+01 1.00e-02 4.81e+01 dihedral pdb=" CA CYS G 119 " pdb=" C CYS G 119 " pdb=" N VAL G 120 " pdb=" CA VAL G 120 " ideal model delta harmonic sigma weight residual -180.00 -146.52 -33.48 0 5.00e+00 4.00e-02 4.48e+01 ... (remaining 16472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 4103 0.286 - 0.572: 9 0.572 - 0.858: 4 0.858 - 1.144: 1 1.144 - 1.429: 1 Chirality restraints: 4118 Sorted by residual: chirality pdb=" C1 BMA f 3 " pdb=" O4 NAG f 2 " pdb=" C2 BMA f 3 " pdb=" O5 BMA f 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.77e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN E 160 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.97 -1.43 2.00e-01 2.50e+01 5.11e+01 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.99e+01 ... (remaining 4115 not shown) Planarity restraints: 3247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 160 " -0.032 2.00e-02 2.50e+03 3.69e-02 1.70e+01 pdb=" CG ASN E 160 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN E 160 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN E 160 " 0.062 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 120 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" C VAL G 120 " 0.048 2.00e-02 2.50e+03 pdb=" O VAL G 120 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS G 121 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN E 318 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO E 319 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 319 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 319 " -0.036 5.00e-02 4.00e+02 ... (remaining 3244 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 213 2.53 - 3.12: 17336 3.12 - 3.71: 28722 3.71 - 4.31: 41658 4.31 - 4.90: 65854 Nonbonded interactions: 153783 Sorted by model distance: nonbonded pdb=" O3 NAGKA 1 " pdb=" O5 NAGKA 2 " model vdw 1.932 3.040 nonbonded pdb=" O3 NAGNA 1 " pdb=" O5 NAGNA 2 " model vdw 2.052 3.040 nonbonded pdb=" O3 NAG e 1 " pdb=" O5 NAG e 2 " model vdw 2.059 3.040 nonbonded pdb=" O3 NAG 2 1 " pdb=" O5 NAG 2 2 " model vdw 2.061 3.040 nonbonded pdb=" O3 NAG T 2 " pdb=" O5 BMA T 3 " model vdw 2.099 3.040 ... (remaining 153778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '4' selection = chain '9' selection = chain 'DA' selection = chain 'GA' selection = chain 'LA' selection = chain 'M' selection = chain 'P' selection = chain 'PA' selection = chain 'T' selection = chain 'X' selection = chain 'a' selection = chain 'j' selection = chain 'o' selection = chain 's' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain '6' selection = chain 'HA' selection = chain 'J' selection = chain 'MA' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'RA' selection = chain 'U' selection = chain 'Z' selection = chain 'b' selection = chain 'k' selection = chain 'l' selection = chain 'w' } ncs_group { reference = chain '2' selection = chain '3' selection = chain '8' selection = chain 'AA' selection = chain 'NA' selection = chain 'OA' selection = chain 'S' selection = chain 'h' selection = chain 'i' selection = chain 'n' selection = chain 'p' } ncs_group { reference = chain '5' selection = chain '7' selection = chain 'BA' selection = chain 'CA' selection = chain 'D' selection = chain 'FA' selection = chain 'I' selection = chain 'JA' selection = chain 'K' selection = chain 'O' selection = chain 'QA' selection = chain 'V' selection = chain 'W' selection = chain 'd' selection = chain 'g' selection = chain 'm' selection = chain 'q' selection = chain 'r' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 512 through 557 or resid 572 through 664)) selection = (chain 'C' and (resid 512 through 557 or resid 572 through 664)) } ncs_group { reference = (chain 'E' and resid 33 through 505) selection = (chain 'F' and resid 33 through 505) selection = (chain 'G' and resid 33 through 505) } ncs_group { reference = (chain 'EA' and (resid 1 or resid 4 through 6)) selection = (chain 'IA' and (resid 2 or resid 5 through 7)) selection = (chain 'Y' and (resid 1 or resid 4 through 6)) selection = (chain 't' and (resid 1 or resid 4 through 6)) selection = (chain 'x' and (resid 2 or resid 5 through 7)) selection = (chain 'z' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'KA' selection = chain 'c' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 48.970 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.220 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.007 0.150 21545 Z= 0.334 Angle : 1.135 14.082 29813 Z= 0.434 Chirality : 0.069 1.429 4118 Planarity : 0.003 0.065 3172 Dihedral : 24.441 125.756 12342 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.97 % Favored : 91.94 % Rotamer: Outliers : 0.69 % Allowed : 0.80 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.76 (0.19), residues: 2109 helix: 1.71 (0.28), residues: 354 sheet: -0.33 (0.23), residues: 551 loop : -1.31 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 610 HIS 0.003 0.001 HIS E 411 PHE 0.015 0.001 PHE L 10 TYR 0.010 0.001 TYR H 101 ARG 0.005 0.000 ARG G 190 Details of bonding type rmsd link_NAG-ASN : bond 0.01791 ( 75) link_NAG-ASN : angle 3.18598 ( 225) link_ALPHA1-6 : bond 0.00517 ( 34) link_ALPHA1-6 : angle 1.65619 ( 102) link_BETA1-4 : bond 0.00564 ( 133) link_BETA1-4 : angle 2.10009 ( 399) link_ALPHA1-2 : bond 0.00532 ( 11) link_ALPHA1-2 : angle 2.46328 ( 33) link_ALPHA1-3 : bond 0.00568 ( 48) link_ALPHA1-3 : angle 1.92684 ( 144) hydrogen bonds : bond 0.28177 ( 526) hydrogen bonds : angle 8.81945 ( 1374) SS BOND : bond 0.00272 ( 41) SS BOND : angle 1.80948 ( 82) covalent geometry : bond 0.00670 (21203) covalent geometry : angle 1.07069 (28828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 350 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9198 (t0) cc_final: 0.8975 (t0) REVERT: A 651 ILE cc_start: 0.8629 (mt) cc_final: 0.7661 (mm) REVERT: C 585 LYS cc_start: 0.8618 (tptp) cc_final: 0.8317 (tptp) REVERT: C 624 ASN cc_start: 0.8495 (m-40) cc_final: 0.7993 (t0) REVERT: G 161 MET cc_start: 0.8335 (tmm) cc_final: 0.7947 (tmm) REVERT: G 354 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7564 (p0) REVERT: H 33 ASP cc_start: 0.8662 (m-30) cc_final: 0.8283 (t0) REVERT: H 110 HIS cc_start: 0.6301 (m-70) cc_final: 0.5838 (p-80) REVERT: L 32 TYR cc_start: 0.8358 (m-80) cc_final: 0.8057 (m-80) outliers start: 13 outliers final: 5 residues processed: 363 average time/residue: 0.3481 time to fit residues: 186.7369 Evaluate side-chains 166 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 165 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 629 GLN B 602 GLN B 629 GLN E 103 GLN E 254 GLN E 419 HIS F 328 GLN ** G 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN L 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.066039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049040 restraints weight = 114332.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.050657 restraints weight = 61902.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.051701 restraints weight = 42887.119| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21545 Z= 0.185 Angle : 1.012 12.633 29813 Z= 0.432 Chirality : 0.053 0.596 4118 Planarity : 0.005 0.052 3172 Dihedral : 20.222 119.758 8339 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.11 % Favored : 92.79 % Rotamer: Outliers : 0.27 % Allowed : 5.01 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.07 (0.18), residues: 2109 helix: 1.13 (0.26), residues: 372 sheet: -0.67 (0.22), residues: 577 loop : -1.36 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 108 HIS 0.004 0.001 HIS H 35 PHE 0.024 0.002 PHE H 100D TYR 0.017 0.001 TYR B 658 ARG 0.013 0.001 ARG B 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00689 ( 75) link_NAG-ASN : angle 3.62943 ( 225) link_ALPHA1-6 : bond 0.00567 ( 34) link_ALPHA1-6 : angle 1.91961 ( 102) link_BETA1-4 : bond 0.00613 ( 133) link_BETA1-4 : angle 2.51942 ( 399) link_ALPHA1-2 : bond 0.00988 ( 11) link_ALPHA1-2 : angle 3.04453 ( 33) link_ALPHA1-3 : bond 0.00996 ( 48) link_ALPHA1-3 : angle 2.61341 ( 144) hydrogen bonds : bond 0.06776 ( 526) hydrogen bonds : angle 6.59244 ( 1374) SS BOND : bond 0.00348 ( 41) SS BOND : angle 1.18082 ( 82) covalent geometry : bond 0.00382 (21203) covalent geometry : angle 0.89769 (28828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9546 (t0) cc_final: 0.9135 (t0) REVERT: A 630 GLU cc_start: 0.9510 (pt0) cc_final: 0.9278 (pt0) REVERT: A 659 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8674 (pm20) REVERT: B 589 ASP cc_start: 0.9250 (m-30) cc_final: 0.8807 (t0) REVERT: B 640 GLU cc_start: 0.8394 (pm20) cc_final: 0.7912 (pm20) REVERT: C 576 LEU cc_start: 0.8601 (mm) cc_final: 0.7689 (mm) REVERT: C 585 LYS cc_start: 0.9084 (tptp) cc_final: 0.8805 (tptp) REVERT: E 98 ASN cc_start: 0.8599 (t0) cc_final: 0.7703 (t0) REVERT: F 207 LYS cc_start: 0.8888 (mttm) cc_final: 0.8625 (mmmt) REVERT: F 294 MET cc_start: 0.8904 (tmm) cc_final: 0.8645 (tmm) REVERT: G 98 ASN cc_start: 0.8714 (t0) cc_final: 0.8082 (t0) REVERT: G 161 MET cc_start: 0.8827 (tmm) cc_final: 0.7686 (tmm) REVERT: H 33 ASP cc_start: 0.9057 (m-30) cc_final: 0.8818 (t0) REVERT: H 36 TRP cc_start: 0.8781 (m100) cc_final: 0.7821 (m100) REVERT: H 48 MET cc_start: 0.6679 (mtp) cc_final: 0.6173 (mtp) REVERT: H 80 MET cc_start: 0.8131 (ptm) cc_final: 0.7562 (ptm) REVERT: H 100 TYR cc_start: 0.8478 (t80) cc_final: 0.8254 (t80) REVERT: H 100 LEU cc_start: 0.9442 (tt) cc_final: 0.9207 (tt) REVERT: H 110 HIS cc_start: 0.7584 (m-70) cc_final: 0.6670 (p-80) REVERT: L 32 TYR cc_start: 0.8802 (m-80) cc_final: 0.7992 (m-80) outliers start: 5 outliers final: 3 residues processed: 219 average time/residue: 0.3131 time to fit residues: 105.7418 Evaluate side-chains 152 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 123 optimal weight: 0.0060 chunk 185 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 176 optimal weight: 0.0010 chunk 37 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 629 GLN A 653 GLN B 575 ASN B 629 GLN C 551 GLN C 602 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN ** E 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 392 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.066068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.049237 restraints weight = 114665.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.050855 restraints weight = 61877.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.051900 restraints weight = 42797.232| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21545 Z= 0.155 Angle : 0.918 10.698 29813 Z= 0.392 Chirality : 0.051 0.491 4118 Planarity : 0.004 0.055 3172 Dihedral : 17.149 113.362 8339 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.60 % Rotamer: Outliers : 0.27 % Allowed : 4.21 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.26 (0.18), residues: 2109 helix: 0.81 (0.26), residues: 390 sheet: -0.82 (0.22), residues: 583 loop : -1.43 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 176 HIS 0.004 0.001 HIS G 352 PHE 0.025 0.002 PHE C 522 TYR 0.018 0.001 TYR B 586 ARG 0.009 0.001 ARG A 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00431 ( 75) link_NAG-ASN : angle 2.94013 ( 225) link_ALPHA1-6 : bond 0.00708 ( 34) link_ALPHA1-6 : angle 1.86446 ( 102) link_BETA1-4 : bond 0.00585 ( 133) link_BETA1-4 : angle 2.14671 ( 399) link_ALPHA1-2 : bond 0.00888 ( 11) link_ALPHA1-2 : angle 2.93733 ( 33) link_ALPHA1-3 : bond 0.01144 ( 48) link_ALPHA1-3 : angle 1.96341 ( 144) hydrogen bonds : bond 0.05401 ( 526) hydrogen bonds : angle 5.91130 ( 1374) SS BOND : bond 0.00308 ( 41) SS BOND : angle 1.50764 ( 82) covalent geometry : bond 0.00315 (21203) covalent geometry : angle 0.83172 (28828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 199 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8606 (pm20) REVERT: A 594 ASN cc_start: 0.9571 (t0) cc_final: 0.9130 (t0) REVERT: A 636 ASP cc_start: 0.8473 (t0) cc_final: 0.8186 (m-30) REVERT: A 651 ILE cc_start: 0.8313 (mm) cc_final: 0.7890 (mm) REVERT: B 589 ASP cc_start: 0.9241 (m-30) cc_final: 0.8817 (t70) REVERT: B 658 TYR cc_start: 0.5818 (p90) cc_final: 0.5571 (p90) REVERT: E 98 ASN cc_start: 0.8386 (t0) cc_final: 0.7375 (t0) REVERT: E 147 MET cc_start: 0.8626 (mtp) cc_final: 0.8412 (mtp) REVERT: E 471 MET cc_start: 0.8698 (mmm) cc_final: 0.8373 (mmm) REVERT: F 129 MET cc_start: 0.8845 (mtp) cc_final: 0.8575 (mtp) REVERT: F 207 LYS cc_start: 0.8901 (mttm) cc_final: 0.8641 (mmmt) REVERT: F 251 MET cc_start: 0.8798 (mmm) cc_final: 0.8559 (tpt) REVERT: F 294 MET cc_start: 0.8968 (tmm) cc_final: 0.8647 (tmm) REVERT: F 374 MET cc_start: 0.8201 (ppp) cc_final: 0.7802 (ppp) REVERT: F 387 MET cc_start: 0.9236 (mmp) cc_final: 0.8939 (mmm) REVERT: G 98 ASN cc_start: 0.8482 (t0) cc_final: 0.7738 (t0) REVERT: G 161 MET cc_start: 0.8880 (tmm) cc_final: 0.7790 (tmm) REVERT: G 374 MET cc_start: 0.7621 (tmm) cc_final: 0.7152 (tmm) REVERT: G 387 MET cc_start: 0.8979 (mtt) cc_final: 0.8735 (ttt) REVERT: H 35 HIS cc_start: 0.8912 (m90) cc_final: 0.8652 (m-70) REVERT: H 36 TRP cc_start: 0.8764 (m100) cc_final: 0.7305 (m100) REVERT: H 80 MET cc_start: 0.8155 (ptm) cc_final: 0.7652 (ptm) REVERT: H 100 TYR cc_start: 0.8527 (t80) cc_final: 0.8245 (t80) REVERT: H 100 LEU cc_start: 0.9462 (tt) cc_final: 0.9234 (tt) REVERT: H 110 HIS cc_start: 0.7563 (m-70) cc_final: 0.6679 (p-80) REVERT: L 32 TYR cc_start: 0.8763 (m-80) cc_final: 0.7986 (m-80) REVERT: L 89 MET cc_start: 0.8535 (tpt) cc_final: 0.7653 (tpt) outliers start: 5 outliers final: 0 residues processed: 203 average time/residue: 0.3218 time to fit residues: 101.2901 Evaluate side-chains 148 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 137 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 202 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN C 540 GLN ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN E 428 HIS ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN G 254 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 HIS L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.063968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046958 restraints weight = 117168.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.048547 restraints weight = 63170.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049573 restraints weight = 43729.084| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21545 Z= 0.189 Angle : 0.929 12.517 29813 Z= 0.398 Chirality : 0.052 0.453 4118 Planarity : 0.004 0.052 3172 Dihedral : 14.593 109.394 8339 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.84 % Rotamer: Outliers : 0.11 % Allowed : 4.69 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.28 (0.18), residues: 2109 helix: 0.86 (0.26), residues: 390 sheet: -0.96 (0.22), residues: 554 loop : -1.39 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 176 HIS 0.006 0.001 HIS E 419 PHE 0.034 0.002 PHE H 100D TYR 0.014 0.001 TYR H 100C ARG 0.007 0.001 ARG H 100A Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 75) link_NAG-ASN : angle 2.87711 ( 225) link_ALPHA1-6 : bond 0.00924 ( 34) link_ALPHA1-6 : angle 2.02819 ( 102) link_BETA1-4 : bond 0.00537 ( 133) link_BETA1-4 : angle 2.07295 ( 399) link_ALPHA1-2 : bond 0.00797 ( 11) link_ALPHA1-2 : angle 2.90326 ( 33) link_ALPHA1-3 : bond 0.01124 ( 48) link_ALPHA1-3 : angle 2.16609 ( 144) hydrogen bonds : bond 0.05026 ( 526) hydrogen bonds : angle 5.70560 ( 1374) SS BOND : bond 0.00347 ( 41) SS BOND : angle 1.46527 ( 82) covalent geometry : bond 0.00398 (21203) covalent geometry : angle 0.84484 (28828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 1.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 584 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8672 (pm20) REVERT: A 594 ASN cc_start: 0.9584 (t0) cc_final: 0.9029 (t0) REVERT: A 639 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8311 (mt-10) REVERT: B 530 MET cc_start: 0.8605 (tpp) cc_final: 0.7383 (mmm) REVERT: B 589 ASP cc_start: 0.9223 (m-30) cc_final: 0.8787 (t70) REVERT: B 658 TYR cc_start: 0.6056 (p90) cc_final: 0.5659 (p90) REVERT: C 530 MET cc_start: 0.7404 (mtt) cc_final: 0.6645 (mmt) REVERT: C 586 TYR cc_start: 0.9076 (t80) cc_final: 0.8842 (t80) REVERT: E 98 ASN cc_start: 0.8391 (t0) cc_final: 0.7627 (t0) REVERT: E 147 MET cc_start: 0.8666 (mtp) cc_final: 0.8417 (mtp) REVERT: E 161 MET cc_start: 0.8785 (tpp) cc_final: 0.8530 (tpp) REVERT: E 471 MET cc_start: 0.8909 (mmm) cc_final: 0.8650 (mmm) REVERT: F 129 MET cc_start: 0.8386 (mtp) cc_final: 0.8085 (mtp) REVERT: F 207 LYS cc_start: 0.8955 (mttm) cc_final: 0.8746 (mmmt) REVERT: F 237 MET cc_start: 0.8874 (ttm) cc_final: 0.8551 (ttm) REVERT: F 294 MET cc_start: 0.8999 (tmm) cc_final: 0.8614 (tmm) REVERT: F 374 MET cc_start: 0.8302 (ppp) cc_final: 0.7915 (ppp) REVERT: F 471 MET cc_start: 0.9422 (ttp) cc_final: 0.8876 (ttp) REVERT: G 98 ASN cc_start: 0.8582 (t0) cc_final: 0.7980 (t0) REVERT: G 161 MET cc_start: 0.8906 (tmm) cc_final: 0.8495 (tmm) REVERT: G 292 LEU cc_start: 0.8853 (mp) cc_final: 0.8230 (mt) REVERT: G 374 MET cc_start: 0.7976 (tmm) cc_final: 0.7404 (tmm) REVERT: G 387 MET cc_start: 0.8930 (mtt) cc_final: 0.8691 (ttp) REVERT: H 35 HIS cc_start: 0.9014 (m90) cc_final: 0.8486 (m-70) REVERT: H 36 TRP cc_start: 0.8764 (m100) cc_final: 0.7372 (m100) REVERT: H 80 MET cc_start: 0.8303 (ptm) cc_final: 0.8022 (ptm) REVERT: H 100 ARG cc_start: 0.7570 (ttt180) cc_final: 0.6904 (ttp80) REVERT: H 110 HIS cc_start: 0.7305 (m-70) cc_final: 0.6565 (p-80) REVERT: L 32 TYR cc_start: 0.8869 (m-80) cc_final: 0.7969 (m-80) REVERT: L 89 MET cc_start: 0.8448 (tpt) cc_final: 0.7770 (tpt) outliers start: 2 outliers final: 0 residues processed: 172 average time/residue: 0.3317 time to fit residues: 89.6335 Evaluate side-chains 129 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 173 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 199 optimal weight: 30.0000 chunk 88 optimal weight: 0.0870 chunk 177 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS G 254 GLN G 392 ASN L 27 HIS L 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.063637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.046532 restraints weight = 117283.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048113 restraints weight = 62747.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.049115 restraints weight = 43442.091| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21545 Z= 0.178 Angle : 0.891 11.278 29813 Z= 0.383 Chirality : 0.050 0.442 4118 Planarity : 0.004 0.084 3172 Dihedral : 13.215 105.874 8339 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.54 % Favored : 92.37 % Rotamer: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.32 (0.18), residues: 2109 helix: 0.95 (0.27), residues: 386 sheet: -0.95 (0.24), residues: 455 loop : -1.48 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 258 HIS 0.005 0.001 HIS E 428 PHE 0.042 0.002 PHE H 100D TYR 0.010 0.001 TYR E 192 ARG 0.008 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 75) link_NAG-ASN : angle 2.75354 ( 225) link_ALPHA1-6 : bond 0.00932 ( 34) link_ALPHA1-6 : angle 1.88624 ( 102) link_BETA1-4 : bond 0.00534 ( 133) link_BETA1-4 : angle 1.92171 ( 399) link_ALPHA1-2 : bond 0.00935 ( 11) link_ALPHA1-2 : angle 2.91559 ( 33) link_ALPHA1-3 : bond 0.01146 ( 48) link_ALPHA1-3 : angle 1.96926 ( 144) hydrogen bonds : bond 0.04540 ( 526) hydrogen bonds : angle 5.46686 ( 1374) SS BOND : bond 0.00334 ( 41) SS BOND : angle 1.25733 ( 82) covalent geometry : bond 0.00370 (21203) covalent geometry : angle 0.81553 (28828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9597 (t0) cc_final: 0.9121 (t0) REVERT: B 574 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8313 (mttt) REVERT: B 589 ASP cc_start: 0.9267 (m-30) cc_final: 0.8849 (t70) REVERT: B 658 TYR cc_start: 0.6005 (p90) cc_final: 0.5337 (p90) REVERT: C 530 MET cc_start: 0.7470 (mtt) cc_final: 0.6629 (mmt) REVERT: E 98 ASN cc_start: 0.8338 (t0) cc_final: 0.7582 (t0) REVERT: E 147 MET cc_start: 0.8618 (mtp) cc_final: 0.8364 (mtp) REVERT: E 161 MET cc_start: 0.8669 (tpp) cc_final: 0.8348 (tpp) REVERT: E 377 ASN cc_start: 0.8440 (t0) cc_final: 0.7965 (m-40) REVERT: F 69 TRP cc_start: 0.7499 (p90) cc_final: 0.7085 (p90) REVERT: F 129 MET cc_start: 0.8495 (mtp) cc_final: 0.8161 (mtp) REVERT: F 207 LYS cc_start: 0.9000 (mttm) cc_final: 0.8722 (mmmt) REVERT: F 237 MET cc_start: 0.8931 (ttm) cc_final: 0.8683 (tpp) REVERT: F 292 LEU cc_start: 0.9183 (mp) cc_final: 0.8716 (mt) REVERT: F 294 MET cc_start: 0.8998 (tmm) cc_final: 0.8610 (tmm) REVERT: F 310 MET cc_start: 0.8580 (ppp) cc_final: 0.7996 (ppp) REVERT: F 374 MET cc_start: 0.8350 (ppp) cc_final: 0.8130 (ppp) REVERT: F 471 MET cc_start: 0.9269 (ttp) cc_final: 0.8849 (ttp) REVERT: G 98 ASN cc_start: 0.8644 (t0) cc_final: 0.8145 (t0) REVERT: G 161 MET cc_start: 0.8915 (tmm) cc_final: 0.8526 (tmm) REVERT: G 292 LEU cc_start: 0.9059 (mp) cc_final: 0.8400 (mt) REVERT: G 374 MET cc_start: 0.7958 (tmm) cc_final: 0.7474 (tmm) REVERT: G 387 MET cc_start: 0.8900 (mtt) cc_final: 0.8696 (ttm) REVERT: H 35 HIS cc_start: 0.9038 (m90) cc_final: 0.8638 (m-70) REVERT: H 48 MET cc_start: 0.6922 (mtp) cc_final: 0.6141 (mtp) REVERT: H 80 MET cc_start: 0.8456 (ptm) cc_final: 0.7904 (ptm) REVERT: H 110 HIS cc_start: 0.7347 (m-70) cc_final: 0.6565 (p-80) REVERT: L 32 TYR cc_start: 0.8918 (m-80) cc_final: 0.7991 (m-80) REVERT: L 89 MET cc_start: 0.8739 (tpt) cc_final: 0.8468 (mmm) outliers start: 1 outliers final: 1 residues processed: 170 average time/residue: 0.3107 time to fit residues: 82.8371 Evaluate side-chains 127 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 13 optimal weight: 10.0000 chunk 185 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 653 GLN C 540 GLN C 551 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN F 151 GLN G 254 GLN G 428 HIS L 27 HIS L 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.063998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.047124 restraints weight = 115639.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.048718 restraints weight = 61630.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049733 restraints weight = 42477.042| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21545 Z= 0.146 Angle : 0.861 11.469 29813 Z= 0.367 Chirality : 0.050 0.433 4118 Planarity : 0.004 0.052 3172 Dihedral : 12.217 104.249 8339 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.16 % Favored : 92.79 % Rotamer: Outliers : 0.05 % Allowed : 2.45 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.38 (0.18), residues: 2109 helix: 0.70 (0.26), residues: 406 sheet: -0.87 (0.26), residues: 401 loop : -1.52 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 338 HIS 0.002 0.001 HIS F 352 PHE 0.017 0.001 PHE C 600 TYR 0.019 0.001 TYR C 586 ARG 0.009 0.000 ARG H 100A Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 75) link_NAG-ASN : angle 2.65733 ( 225) link_ALPHA1-6 : bond 0.00977 ( 34) link_ALPHA1-6 : angle 1.83417 ( 102) link_BETA1-4 : bond 0.00524 ( 133) link_BETA1-4 : angle 1.85842 ( 399) link_ALPHA1-2 : bond 0.01018 ( 11) link_ALPHA1-2 : angle 2.79262 ( 33) link_ALPHA1-3 : bond 0.01151 ( 48) link_ALPHA1-3 : angle 1.89613 ( 144) hydrogen bonds : bond 0.04302 ( 526) hydrogen bonds : angle 5.36864 ( 1374) SS BOND : bond 0.00294 ( 41) SS BOND : angle 1.39115 ( 82) covalent geometry : bond 0.00298 (21203) covalent geometry : angle 0.78667 (28828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9601 (t0) cc_final: 0.9111 (t0) REVERT: A 653 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8478 (pp30) REVERT: B 574 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8334 (mtpt) REVERT: B 588 LYS cc_start: 0.9456 (tmtt) cc_final: 0.9129 (mtpp) REVERT: B 589 ASP cc_start: 0.9213 (m-30) cc_final: 0.8885 (m-30) REVERT: B 596 TRP cc_start: 0.9259 (m-10) cc_final: 0.8604 (m-10) REVERT: B 658 TYR cc_start: 0.5965 (p90) cc_final: 0.5260 (p90) REVERT: C 530 MET cc_start: 0.7434 (mtt) cc_final: 0.6613 (mmt) REVERT: E 98 ASN cc_start: 0.8235 (t0) cc_final: 0.7508 (t0) REVERT: E 147 MET cc_start: 0.8615 (mtp) cc_final: 0.8350 (mtp) REVERT: E 161 MET cc_start: 0.8659 (tpp) cc_final: 0.8157 (tpp) REVERT: E 377 ASN cc_start: 0.8436 (t0) cc_final: 0.7964 (m-40) REVERT: F 129 MET cc_start: 0.8435 (mtp) cc_final: 0.8139 (mtp) REVERT: F 207 LYS cc_start: 0.8940 (mttm) cc_final: 0.8650 (mmmt) REVERT: F 237 MET cc_start: 0.8916 (ttm) cc_final: 0.8638 (ttm) REVERT: F 292 LEU cc_start: 0.9174 (mp) cc_final: 0.8852 (mt) REVERT: F 294 MET cc_start: 0.8927 (tmm) cc_final: 0.8539 (tmm) REVERT: F 374 MET cc_start: 0.8314 (ppp) cc_final: 0.8103 (ppp) REVERT: F 471 MET cc_start: 0.9337 (ttp) cc_final: 0.8931 (ttp) REVERT: G 98 ASN cc_start: 0.8475 (t0) cc_final: 0.8099 (t0) REVERT: G 161 MET cc_start: 0.8982 (tmm) cc_final: 0.8585 (tmm) REVERT: G 251 MET cc_start: 0.8476 (tmm) cc_final: 0.8235 (tmm) REVERT: G 374 MET cc_start: 0.7973 (tmm) cc_final: 0.7400 (tmm) REVERT: G 387 MET cc_start: 0.8850 (mtt) cc_final: 0.8577 (ttp) REVERT: H 51 MET cc_start: 0.9168 (tmm) cc_final: 0.8658 (tmm) REVERT: H 54 LYS cc_start: 0.8507 (tptt) cc_final: 0.8284 (tptm) REVERT: H 80 MET cc_start: 0.8384 (ptm) cc_final: 0.7962 (ptm) REVERT: H 110 HIS cc_start: 0.7317 (m-70) cc_final: 0.6479 (p-80) REVERT: L 32 TYR cc_start: 0.8876 (m-80) cc_final: 0.8038 (m-80) REVERT: L 89 MET cc_start: 0.8751 (tpt) cc_final: 0.8479 (mmm) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.3236 time to fit residues: 88.5186 Evaluate side-chains 126 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 78 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 197 optimal weight: 0.0870 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.063971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.046921 restraints weight = 115985.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048475 restraints weight = 62501.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049467 restraints weight = 43396.715| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21545 Z= 0.151 Angle : 0.861 15.414 29813 Z= 0.366 Chirality : 0.049 0.424 4118 Planarity : 0.004 0.059 3172 Dihedral : 11.616 102.996 8339 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.16 % Favored : 92.70 % Rotamer: Outliers : 0.05 % Allowed : 1.65 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.38 (0.18), residues: 2109 helix: 0.71 (0.26), residues: 406 sheet: -0.86 (0.24), residues: 451 loop : -1.54 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 623 HIS 0.004 0.001 HIS F 274 PHE 0.020 0.002 PHE H 29 TYR 0.010 0.001 TYR E 384 ARG 0.012 0.001 ARG F 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 75) link_NAG-ASN : angle 2.94492 ( 225) link_ALPHA1-6 : bond 0.00980 ( 34) link_ALPHA1-6 : angle 1.85420 ( 102) link_BETA1-4 : bond 0.00524 ( 133) link_BETA1-4 : angle 1.83158 ( 399) link_ALPHA1-2 : bond 0.00957 ( 11) link_ALPHA1-2 : angle 2.74179 ( 33) link_ALPHA1-3 : bond 0.01104 ( 48) link_ALPHA1-3 : angle 1.84081 ( 144) hydrogen bonds : bond 0.04141 ( 526) hydrogen bonds : angle 5.30631 ( 1374) SS BOND : bond 0.00299 ( 41) SS BOND : angle 1.30212 ( 82) covalent geometry : bond 0.00311 (21203) covalent geometry : angle 0.78069 (28828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9607 (t0) cc_final: 0.9137 (t0) REVERT: B 574 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8292 (mtpt) REVERT: B 657 MET cc_start: 0.8106 (ppp) cc_final: 0.7876 (ppp) REVERT: B 658 TYR cc_start: 0.6143 (p90) cc_final: 0.5143 (p90) REVERT: C 530 MET cc_start: 0.7421 (mtt) cc_final: 0.6637 (mmt) REVERT: E 98 ASN cc_start: 0.8194 (t0) cc_final: 0.7471 (t0) REVERT: E 147 MET cc_start: 0.8638 (mtp) cc_final: 0.8369 (mtp) REVERT: E 161 MET cc_start: 0.8570 (tpp) cc_final: 0.8224 (tpp) REVERT: E 374 MET cc_start: 0.8509 (ttm) cc_final: 0.8306 (ttp) REVERT: E 377 ASN cc_start: 0.8393 (t0) cc_final: 0.8011 (m-40) REVERT: E 471 MET cc_start: 0.8776 (ttm) cc_final: 0.8297 (ttm) REVERT: F 129 MET cc_start: 0.8288 (mtp) cc_final: 0.7964 (mtp) REVERT: F 207 LYS cc_start: 0.8965 (mttm) cc_final: 0.8657 (mmmt) REVERT: F 237 MET cc_start: 0.8716 (ttm) cc_final: 0.8465 (ttm) REVERT: F 294 MET cc_start: 0.8935 (tmm) cc_final: 0.8542 (tmm) REVERT: F 310 MET cc_start: 0.8654 (ppp) cc_final: 0.8401 (ppp) REVERT: F 374 MET cc_start: 0.8363 (ppp) cc_final: 0.7901 (ppp) REVERT: G 98 ASN cc_start: 0.8504 (t0) cc_final: 0.7996 (t0) REVERT: G 161 MET cc_start: 0.8993 (tmm) cc_final: 0.8599 (tmm) REVERT: G 251 MET cc_start: 0.8486 (tmm) cc_final: 0.8191 (tmm) REVERT: G 374 MET cc_start: 0.8062 (tmm) cc_final: 0.7459 (tmm) REVERT: G 387 MET cc_start: 0.8884 (mtt) cc_final: 0.8580 (ttp) REVERT: H 80 MET cc_start: 0.8359 (ptm) cc_final: 0.7938 (ptm) REVERT: H 110 HIS cc_start: 0.7373 (m-70) cc_final: 0.6567 (p-80) REVERT: L 32 TYR cc_start: 0.8892 (m-80) cc_final: 0.8068 (m-80) REVERT: L 89 MET cc_start: 0.8753 (tpt) cc_final: 0.8301 (tpt) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.3240 time to fit residues: 85.0430 Evaluate side-chains 125 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 199 optimal weight: 40.0000 chunk 152 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN C 540 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN G 254 GLN G 428 HIS L 27 HIS L 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.064580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.047792 restraints weight = 117674.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.049329 restraints weight = 63939.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050311 restraints weight = 44588.896| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21545 Z= 0.148 Angle : 0.843 10.326 29813 Z= 0.361 Chirality : 0.048 0.414 4118 Planarity : 0.004 0.052 3172 Dihedral : 10.904 101.399 8339 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.34 (0.18), residues: 2109 helix: 0.73 (0.26), residues: 405 sheet: -0.76 (0.26), residues: 402 loop : -1.52 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 258 HIS 0.004 0.001 HIS F 195 PHE 0.018 0.001 PHE C 600 TYR 0.012 0.001 TYR E 384 ARG 0.009 0.000 ARG B 633 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 75) link_NAG-ASN : angle 2.78128 ( 225) link_ALPHA1-6 : bond 0.01020 ( 34) link_ALPHA1-6 : angle 1.83495 ( 102) link_BETA1-4 : bond 0.00528 ( 133) link_BETA1-4 : angle 1.78877 ( 399) link_ALPHA1-2 : bond 0.00930 ( 11) link_ALPHA1-2 : angle 2.68489 ( 33) link_ALPHA1-3 : bond 0.01074 ( 48) link_ALPHA1-3 : angle 1.78557 ( 144) hydrogen bonds : bond 0.04058 ( 526) hydrogen bonds : angle 5.24403 ( 1374) SS BOND : bond 0.00622 ( 41) SS BOND : angle 1.31579 ( 82) covalent geometry : bond 0.00303 (21203) covalent geometry : angle 0.76748 (28828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9621 (t0) cc_final: 0.9163 (t0) REVERT: B 530 MET cc_start: 0.8445 (mmm) cc_final: 0.8067 (mmm) REVERT: B 574 LYS cc_start: 0.8409 (mtpp) cc_final: 0.8181 (mtpt) REVERT: B 588 LYS cc_start: 0.9473 (tmtt) cc_final: 0.9120 (mtpp) REVERT: B 589 ASP cc_start: 0.9235 (m-30) cc_final: 0.8912 (m-30) REVERT: B 654 GLU cc_start: 0.8568 (pp20) cc_final: 0.8023 (pp20) REVERT: B 657 MET cc_start: 0.8154 (ppp) cc_final: 0.7939 (ppp) REVERT: B 658 TYR cc_start: 0.6064 (p90) cc_final: 0.5231 (p90) REVERT: C 530 MET cc_start: 0.7405 (mtt) cc_final: 0.6613 (mmt) REVERT: C 538 THR cc_start: 0.9134 (m) cc_final: 0.8890 (m) REVERT: C 657 MET cc_start: 0.8679 (ptp) cc_final: 0.8445 (ptp) REVERT: E 98 ASN cc_start: 0.8225 (t0) cc_final: 0.7655 (t0) REVERT: E 129 MET cc_start: 0.8306 (mtt) cc_final: 0.8066 (mtp) REVERT: E 147 MET cc_start: 0.8561 (mtp) cc_final: 0.8309 (mtp) REVERT: E 161 MET cc_start: 0.8471 (tpp) cc_final: 0.8198 (tpp) REVERT: E 377 ASN cc_start: 0.8379 (t0) cc_final: 0.7988 (m-40) REVERT: F 69 TRP cc_start: 0.7287 (p90) cc_final: 0.6836 (p90) REVERT: F 129 MET cc_start: 0.8353 (mtp) cc_final: 0.8097 (mtp) REVERT: F 207 LYS cc_start: 0.8836 (mttm) cc_final: 0.8573 (mmmt) REVERT: F 237 MET cc_start: 0.8661 (ttm) cc_final: 0.8440 (ttm) REVERT: F 294 MET cc_start: 0.8929 (tmm) cc_final: 0.8577 (tmm) REVERT: F 310 MET cc_start: 0.8642 (ppp) cc_final: 0.8431 (ppp) REVERT: F 374 MET cc_start: 0.8495 (ppp) cc_final: 0.8019 (ppp) REVERT: F 471 MET cc_start: 0.9232 (ttp) cc_final: 0.8766 (ttp) REVERT: G 98 ASN cc_start: 0.8472 (t0) cc_final: 0.8099 (t0) REVERT: G 161 MET cc_start: 0.8981 (tmm) cc_final: 0.8603 (tmm) REVERT: G 251 MET cc_start: 0.8435 (tmm) cc_final: 0.8144 (tmm) REVERT: G 374 MET cc_start: 0.8036 (tmm) cc_final: 0.7724 (tmm) REVERT: H 80 MET cc_start: 0.8385 (ptm) cc_final: 0.7919 (ptm) REVERT: H 110 HIS cc_start: 0.7350 (m-70) cc_final: 0.6520 (p-80) REVERT: L 32 TYR cc_start: 0.8860 (m-80) cc_final: 0.8120 (m-80) REVERT: L 89 MET cc_start: 0.8637 (tpt) cc_final: 0.8168 (tpt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.3070 time to fit residues: 80.5009 Evaluate side-chains 124 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 201 optimal weight: 0.1980 chunk 59 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 177 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN C 540 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN G 254 GLN G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.064494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047804 restraints weight = 116674.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.049318 restraints weight = 64193.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.050272 restraints weight = 45046.386| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21545 Z= 0.142 Angle : 0.835 10.218 29813 Z= 0.358 Chirality : 0.048 0.428 4118 Planarity : 0.004 0.052 3172 Dihedral : 10.395 99.845 8339 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.25 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.29 (0.18), residues: 2109 helix: 0.73 (0.26), residues: 407 sheet: -0.89 (0.23), residues: 516 loop : -1.43 (0.18), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 596 HIS 0.002 0.001 HIS F 352 PHE 0.020 0.002 PHE C 519 TYR 0.013 0.001 TYR G 270 ARG 0.007 0.000 ARG H 100A Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 75) link_NAG-ASN : angle 2.73664 ( 225) link_ALPHA1-6 : bond 0.01026 ( 34) link_ALPHA1-6 : angle 1.77452 ( 102) link_BETA1-4 : bond 0.00524 ( 133) link_BETA1-4 : angle 1.77475 ( 399) link_ALPHA1-2 : bond 0.00896 ( 11) link_ALPHA1-2 : angle 2.64980 ( 33) link_ALPHA1-3 : bond 0.01041 ( 48) link_ALPHA1-3 : angle 1.75673 ( 144) hydrogen bonds : bond 0.03878 ( 526) hydrogen bonds : angle 5.18308 ( 1374) SS BOND : bond 0.00281 ( 41) SS BOND : angle 1.12855 ( 82) covalent geometry : bond 0.00292 (21203) covalent geometry : angle 0.76166 (28828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9639 (t0) cc_final: 0.9195 (t0) REVERT: A 630 GLU cc_start: 0.9448 (pt0) cc_final: 0.9165 (pt0) REVERT: B 530 MET cc_start: 0.8225 (mmm) cc_final: 0.7807 (mmm) REVERT: B 548 ILE cc_start: 0.9468 (mm) cc_final: 0.9264 (tp) REVERT: B 574 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8067 (mtpt) REVERT: B 588 LYS cc_start: 0.9495 (tmtt) cc_final: 0.9125 (mtpp) REVERT: B 589 ASP cc_start: 0.9239 (m-30) cc_final: 0.8926 (m-30) REVERT: C 530 MET cc_start: 0.7309 (mtt) cc_final: 0.6574 (mmt) REVERT: C 538 THR cc_start: 0.9073 (m) cc_final: 0.8858 (m) REVERT: E 98 ASN cc_start: 0.8161 (t0) cc_final: 0.7300 (t0) REVERT: E 129 MET cc_start: 0.8306 (mtt) cc_final: 0.8084 (mtp) REVERT: E 147 MET cc_start: 0.8529 (mtp) cc_final: 0.8291 (mtp) REVERT: E 161 MET cc_start: 0.8455 (tpp) cc_final: 0.8104 (tpp) REVERT: E 294 MET cc_start: 0.8932 (ttm) cc_final: 0.8245 (tpp) REVERT: E 368 ASP cc_start: 0.9578 (m-30) cc_final: 0.8925 (p0) REVERT: E 377 ASN cc_start: 0.8350 (t0) cc_final: 0.7988 (m-40) REVERT: E 395 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8421 (mm-30) REVERT: F 129 MET cc_start: 0.8382 (mtp) cc_final: 0.8088 (mtp) REVERT: F 207 LYS cc_start: 0.8797 (mttm) cc_final: 0.8492 (mmmt) REVERT: F 250 MET cc_start: 0.8757 (mmm) cc_final: 0.8311 (mmm) REVERT: F 294 MET cc_start: 0.8925 (tmm) cc_final: 0.8565 (tmm) REVERT: F 310 MET cc_start: 0.8617 (ppp) cc_final: 0.8178 (ppp) REVERT: F 374 MET cc_start: 0.8536 (ppp) cc_final: 0.8053 (ppp) REVERT: F 471 MET cc_start: 0.9267 (ttp) cc_final: 0.8772 (ttp) REVERT: G 67 ASP cc_start: 0.8390 (m-30) cc_final: 0.8085 (m-30) REVERT: G 98 ASN cc_start: 0.8403 (t0) cc_final: 0.8060 (t0) REVERT: G 161 MET cc_start: 0.8965 (tmm) cc_final: 0.8632 (tmm) REVERT: G 251 MET cc_start: 0.8457 (tmm) cc_final: 0.8161 (tmm) REVERT: G 292 LEU cc_start: 0.8926 (mp) cc_final: 0.8357 (mt) REVERT: H 80 MET cc_start: 0.8453 (ptm) cc_final: 0.8073 (ptm) REVERT: H 100 LEU cc_start: 0.9238 (tt) cc_final: 0.9031 (tt) REVERT: H 110 HIS cc_start: 0.7323 (m-70) cc_final: 0.6507 (p-80) REVERT: L 32 TYR cc_start: 0.8828 (m-80) cc_final: 0.8105 (m-80) REVERT: L 89 MET cc_start: 0.8683 (tpt) cc_final: 0.8201 (tpt) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.3029 time to fit residues: 81.8631 Evaluate side-chains 133 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 141 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 197 optimal weight: 0.0030 chunk 42 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 181 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN C 540 GLN C 629 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 208 HIS G 254 GLN G 410 GLN G 411 HIS G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.062972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.046226 restraints weight = 118532.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.047707 restraints weight = 64834.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.048645 restraints weight = 45527.729| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21545 Z= 0.189 Angle : 0.874 11.213 29813 Z= 0.380 Chirality : 0.048 0.423 4118 Planarity : 0.004 0.051 3172 Dihedral : 10.173 101.040 8339 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.73 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.34 (0.18), residues: 2109 helix: 0.71 (0.26), residues: 407 sheet: -0.84 (0.24), residues: 442 loop : -1.49 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 69 HIS 0.004 0.001 HIS G 411 PHE 0.021 0.002 PHE C 600 TYR 0.011 0.001 TYR H 101 ARG 0.008 0.001 ARG H 38 Details of bonding type rmsd link_NAG-ASN : bond 0.00385 ( 75) link_NAG-ASN : angle 2.74115 ( 225) link_ALPHA1-6 : bond 0.01000 ( 34) link_ALPHA1-6 : angle 1.81815 ( 102) link_BETA1-4 : bond 0.00522 ( 133) link_BETA1-4 : angle 1.81167 ( 399) link_ALPHA1-2 : bond 0.00737 ( 11) link_ALPHA1-2 : angle 2.68504 ( 33) link_ALPHA1-3 : bond 0.00966 ( 48) link_ALPHA1-3 : angle 1.87091 ( 144) hydrogen bonds : bond 0.04071 ( 526) hydrogen bonds : angle 5.25262 ( 1374) SS BOND : bond 0.00402 ( 41) SS BOND : angle 1.55516 ( 82) covalent geometry : bond 0.00401 (21203) covalent geometry : angle 0.80134 (28828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4218 Ramachandran restraints generated. 2109 Oldfield, 0 Emsley, 2109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.7930 (mmp) cc_final: 0.7163 (mmt) REVERT: A 594 ASN cc_start: 0.9630 (t0) cc_final: 0.9198 (t0) REVERT: B 574 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8164 (mtpt) REVERT: B 657 MET cc_start: 0.8015 (ppp) cc_final: 0.7757 (ppp) REVERT: B 658 TYR cc_start: 0.5961 (p90) cc_final: 0.5063 (p90) REVERT: C 530 MET cc_start: 0.7305 (mtt) cc_final: 0.6544 (mmt) REVERT: E 98 ASN cc_start: 0.8273 (t0) cc_final: 0.7678 (t0) REVERT: E 129 MET cc_start: 0.8589 (mtt) cc_final: 0.8296 (mtp) REVERT: E 147 MET cc_start: 0.8551 (mtp) cc_final: 0.8284 (mtp) REVERT: E 161 MET cc_start: 0.8630 (tpp) cc_final: 0.8422 (tpp) REVERT: E 294 MET cc_start: 0.9045 (ttm) cc_final: 0.8336 (tpp) REVERT: E 377 ASN cc_start: 0.8268 (t0) cc_final: 0.8025 (m-40) REVERT: F 69 TRP cc_start: 0.7314 (p90) cc_final: 0.6895 (p90) REVERT: F 129 MET cc_start: 0.8445 (mtp) cc_final: 0.8162 (mtp) REVERT: F 194 ASN cc_start: 0.8973 (t0) cc_final: 0.8762 (t0) REVERT: F 207 LYS cc_start: 0.8869 (mttm) cc_final: 0.8598 (mmmt) REVERT: F 237 MET cc_start: 0.8763 (ttm) cc_final: 0.8548 (ttm) REVERT: F 294 MET cc_start: 0.8964 (tmm) cc_final: 0.8595 (tmm) REVERT: F 310 MET cc_start: 0.8658 (ppp) cc_final: 0.8399 (ppp) REVERT: F 374 MET cc_start: 0.8592 (ppp) cc_final: 0.8242 (ppp) REVERT: G 67 ASP cc_start: 0.8517 (m-30) cc_final: 0.8172 (m-30) REVERT: G 98 ASN cc_start: 0.8602 (t0) cc_final: 0.8206 (t0) REVERT: G 161 MET cc_start: 0.8981 (tmm) cc_final: 0.8585 (tmm) REVERT: G 251 MET cc_start: 0.8504 (tmm) cc_final: 0.8140 (tmm) REVERT: H 80 MET cc_start: 0.8554 (ptm) cc_final: 0.8141 (ptm) REVERT: H 100 LEU cc_start: 0.9338 (tt) cc_final: 0.9060 (tt) REVERT: H 110 HIS cc_start: 0.7329 (m-70) cc_final: 0.6412 (p-80) REVERT: L 32 TYR cc_start: 0.8931 (m-80) cc_final: 0.7939 (m-80) REVERT: L 89 MET cc_start: 0.8714 (tpt) cc_final: 0.8256 (tpt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2977 time to fit residues: 76.4160 Evaluate side-chains 124 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 114 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 140 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 174 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN C 540 GLN C 629 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 428 HIS ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.063343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.046284 restraints weight = 119544.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.047761 restraints weight = 65702.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048677 restraints weight = 46530.824| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21545 Z= 0.154 Angle : 0.845 10.556 29813 Z= 0.365 Chirality : 0.047 0.426 4118 Planarity : 0.004 0.052 3172 Dihedral : 9.886 100.915 8339 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.54 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.31 (0.18), residues: 2109 helix: 0.79 (0.27), residues: 407 sheet: -0.90 (0.22), residues: 506 loop : -1.47 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 176 HIS 0.005 0.001 HIS E 428 PHE 0.020 0.002 PHE C 600 TYR 0.011 0.001 TYR E 384 ARG 0.011 0.000 ARG G 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 75) link_NAG-ASN : angle 2.71586 ( 225) link_ALPHA1-6 : bond 0.00995 ( 34) link_ALPHA1-6 : angle 1.70644 ( 102) link_BETA1-4 : bond 0.00516 ( 133) link_BETA1-4 : angle 1.75912 ( 399) link_ALPHA1-2 : bond 0.00777 ( 11) link_ALPHA1-2 : angle 2.65338 ( 33) link_ALPHA1-3 : bond 0.00976 ( 48) link_ALPHA1-3 : angle 1.80832 ( 144) hydrogen bonds : bond 0.03924 ( 526) hydrogen bonds : angle 5.18208 ( 1374) SS BOND : bond 0.00302 ( 41) SS BOND : angle 1.39770 ( 82) covalent geometry : bond 0.00321 (21203) covalent geometry : angle 0.77261 (28828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5379.73 seconds wall clock time: 96 minutes 49.53 seconds (5809.53 seconds total)