Starting phenix.real_space_refine on Sun Aug 24 15:51:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dvd_27735/08_2025/8dvd_27735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvd_27735/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dvd_27735/08_2025/8dvd_27735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvd_27735/08_2025/8dvd_27735.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dvd_27735/08_2025/8dvd_27735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvd_27735/08_2025/8dvd_27735.map" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.33, per 1000 atoms: 0.26 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: 2.49 Conformation dependent library (CDL) restraints added in 750.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.67 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: 3.37 Time building geometry restraints manager: 2.97 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.870 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- 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 : 5.02 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (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 ARG 0.005 0.000 ARG G 190 TYR 0.010 0.001 TYR H 101 PHE 0.015 0.001 PHE L 10 TRP 0.014 0.001 TRP A 610 HIS 0.003 0.001 HIS E 411 Details of bonding type rmsd covalent geometry : bond 0.00670 (21203) covalent geometry : angle 1.07069 (28828) SS BOND : bond 0.00272 ( 41) SS BOND : angle 1.80948 ( 82) hydrogen bonds : bond 0.28177 ( 526) hydrogen bonds : angle 8.81945 ( 1374) 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) 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_NAG-ASN : bond 0.01791 ( 75) link_NAG-ASN : angle 3.18598 ( 225) *********************** 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 : 0.800 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: 0.1491 time to fit residues: 80.7768 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 : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.0980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 B 602 GLN B 629 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN E 419 HIS E 428 HIS F 328 GLN G 254 GLN ** 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 = 0.3545 r_free = 0.3545 target = 0.064926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.048038 restraints weight = 116243.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.049615 restraints weight = 62367.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050639 restraints weight = 43195.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.051265 restraints weight = 34766.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.051623 restraints weight = 30649.054| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21545 Z= 0.215 Angle : 1.066 13.000 29813 Z= 0.454 Chirality : 0.056 0.605 4118 Planarity : 0.005 0.059 3172 Dihedral : 19.875 120.203 8339 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.44 % Favored : 92.46 % Rotamer: Outliers : 0.32 % Allowed : 5.59 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.18), residues: 2109 helix: 0.97 (0.25), residues: 371 sheet: -0.76 (0.22), residues: 577 loop : -1.38 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 579 TYR 0.017 0.002 TYR B 658 PHE 0.026 0.002 PHE H 29 TRP 0.029 0.002 TRP H 108 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00453 (21203) covalent geometry : angle 0.95301 (28828) SS BOND : bond 0.00359 ( 41) SS BOND : angle 1.26917 ( 82) hydrogen bonds : bond 0.06346 ( 526) hydrogen bonds : angle 6.56007 ( 1374) link_ALPHA1-2 : bond 0.00870 ( 11) link_ALPHA1-2 : angle 3.02073 ( 33) link_ALPHA1-3 : bond 0.00997 ( 48) link_ALPHA1-3 : angle 2.85036 ( 144) link_ALPHA1-6 : bond 0.00529 ( 34) link_ALPHA1-6 : angle 2.09293 ( 102) link_BETA1-4 : bond 0.00590 ( 133) link_BETA1-4 : angle 2.65178 ( 399) link_NAG-ASN : bond 0.00551 ( 75) link_NAG-ASN : angle 3.54666 ( 225) *********************** 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 217 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 0.752 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: A 594 ASN cc_start: 0.9587 (t0) cc_final: 0.9212 (t0) REVERT: B 589 ASP cc_start: 0.9221 (m-30) cc_final: 0.8835 (t70) REVERT: B 640 GLU cc_start: 0.8446 (pm20) cc_final: 0.7957 (pm20) REVERT: E 52 LEU cc_start: 0.9381 (mt) cc_final: 0.9172 (mt) REVERT: E 98 ASN cc_start: 0.8681 (t0) cc_final: 0.7768 (t0) REVERT: F 207 LYS cc_start: 0.8943 (mttm) cc_final: 0.8669 (mmmt) REVERT: F 294 MET cc_start: 0.8932 (tmm) cc_final: 0.8658 (tmm) REVERT: G 98 ASN cc_start: 0.8774 (t0) cc_final: 0.8308 (t0) REVERT: G 161 MET cc_start: 0.8834 (tmm) cc_final: 0.7824 (tmm) REVERT: H 33 ASP cc_start: 0.9116 (m-30) cc_final: 0.8851 (t0) REVERT: H 36 TRP cc_start: 0.8853 (m100) cc_final: 0.7963 (m100) REVERT: H 48 MET cc_start: 0.6736 (mtp) cc_final: 0.6223 (mtp) REVERT: H 79 TYR cc_start: 0.8712 (m-10) cc_final: 0.8500 (m-80) REVERT: H 80 MET cc_start: 0.8186 (ptm) cc_final: 0.7620 (ptm) REVERT: H 100 TYR cc_start: 0.8480 (t80) cc_final: 0.8255 (t80) REVERT: H 100 LEU cc_start: 0.9478 (tt) cc_final: 0.9250 (tt) REVERT: H 110 HIS cc_start: 0.7323 (m-70) cc_final: 0.6424 (p-80) REVERT: L 32 TYR cc_start: 0.8838 (m-80) cc_final: 0.7966 (m-80) REVERT: L 89 MET cc_start: 0.8610 (tpt) cc_final: 0.7879 (tpt) outliers start: 6 outliers final: 2 residues processed: 216 average time/residue: 0.1320 time to fit residues: 43.6553 Evaluate side-chains 142 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 178 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 653 GLN B 629 GLN C 540 GLN C 602 GLN E 103 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN ** E 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN G 254 GLN 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 = 0.3521 r_free = 0.3521 target = 0.063733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.046908 restraints weight = 118134.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048409 restraints weight = 65048.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.049364 restraints weight = 45820.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.049951 restraints weight = 37428.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.050286 restraints weight = 33279.035| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21545 Z= 0.212 Angle : 0.964 11.032 29813 Z= 0.417 Chirality : 0.052 0.493 4118 Planarity : 0.005 0.057 3172 Dihedral : 17.009 113.947 8339 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.08 % Rotamer: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.18), residues: 2109 helix: 0.93 (0.26), residues: 390 sheet: -0.98 (0.22), residues: 559 loop : -1.49 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 64 TYR 0.016 0.002 TYR B 586 PHE 0.053 0.002 PHE H 100D TRP 0.026 0.002 TRP G 176 HIS 0.004 0.001 HIS G 352 Details of bonding type rmsd covalent geometry : bond 0.00445 (21203) covalent geometry : angle 0.87790 (28828) SS BOND : bond 0.00336 ( 41) SS BOND : angle 1.78517 ( 82) hydrogen bonds : bond 0.05629 ( 526) hydrogen bonds : angle 6.03733 ( 1374) link_ALPHA1-2 : bond 0.00704 ( 11) link_ALPHA1-2 : angle 2.95157 ( 33) link_ALPHA1-3 : bond 0.01097 ( 48) link_ALPHA1-3 : angle 2.00837 ( 144) link_ALPHA1-6 : bond 0.00650 ( 34) link_ALPHA1-6 : angle 1.98901 ( 102) link_BETA1-4 : bond 0.00593 ( 133) link_BETA1-4 : angle 2.14904 ( 399) link_NAG-ASN : bond 0.00484 ( 75) link_NAG-ASN : angle 3.05146 ( 225) *********************** 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 184 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.681 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: A 584 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8551 (pm20) REVERT: A 594 ASN cc_start: 0.9593 (t0) cc_final: 0.9189 (t0) REVERT: B 589 ASP cc_start: 0.9234 (m-30) cc_final: 0.8838 (t70) REVERT: B 658 TYR cc_start: 0.5810 (p90) cc_final: 0.5563 (p90) REVERT: C 586 TYR cc_start: 0.9274 (t80) cc_final: 0.8895 (t80) REVERT: E 98 ASN cc_start: 0.8624 (t0) cc_final: 0.7918 (t0) REVERT: E 294 MET cc_start: 0.8459 (tmm) cc_final: 0.8176 (tmm) REVERT: F 129 MET cc_start: 0.8952 (mtp) cc_final: 0.8679 (mtp) REVERT: F 207 LYS cc_start: 0.8943 (mttm) cc_final: 0.8693 (mmmt) REVERT: F 294 MET cc_start: 0.8976 (tmm) cc_final: 0.8618 (tmm) REVERT: F 374 MET cc_start: 0.8267 (ppp) cc_final: 0.7943 (ppp) REVERT: G 98 ASN cc_start: 0.8747 (t0) cc_final: 0.8048 (t0) REVERT: G 161 MET cc_start: 0.8932 (tmm) cc_final: 0.7842 (tmm) REVERT: G 292 LEU cc_start: 0.8889 (mp) cc_final: 0.8513 (mt) REVERT: G 374 MET cc_start: 0.7953 (tmm) cc_final: 0.7493 (tmm) REVERT: G 387 MET cc_start: 0.9049 (mtt) cc_final: 0.8748 (ttp) REVERT: H 36 TRP cc_start: 0.8861 (m100) cc_final: 0.7423 (m100) REVERT: H 80 MET cc_start: 0.8149 (ptm) cc_final: 0.7575 (ptm) REVERT: H 100 ARG cc_start: 0.7577 (ttt180) cc_final: 0.7329 (ttp80) REVERT: H 100 TYR cc_start: 0.8844 (t80) cc_final: 0.8625 (t80) REVERT: H 110 HIS cc_start: 0.7361 (m-70) cc_final: 0.7034 (m-70) REVERT: L 32 TYR cc_start: 0.8877 (m-80) cc_final: 0.7954 (m-80) REVERT: L 89 MET cc_start: 0.8517 (tpt) cc_final: 0.7869 (tpt) outliers start: 3 outliers final: 0 residues processed: 182 average time/residue: 0.1350 time to fit residues: 38.2707 Evaluate side-chains 133 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 108 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 171 optimal weight: 0.1980 chunk 43 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 87 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 653 GLN B 653 GLN C 551 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN E 428 HIS F 151 GLN G 254 GLN G 392 ASN 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 = 0.3513 r_free = 0.3513 target = 0.064350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.047402 restraints weight = 114874.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048989 restraints weight = 61707.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.050003 restraints weight = 42652.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050632 restraints weight = 34288.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.050992 restraints weight = 30152.057| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21545 Z= 0.156 Angle : 0.897 12.851 29813 Z= 0.382 Chirality : 0.052 0.462 4118 Planarity : 0.004 0.052 3172 Dihedral : 14.488 109.213 8339 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.84 % Rotamer: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.18), residues: 2109 helix: 0.82 (0.26), residues: 386 sheet: -0.82 (0.22), residues: 545 loop : -1.48 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.015 0.001 TYR B 586 PHE 0.036 0.002 PHE H 100D TRP 0.022 0.001 TRP F 258 HIS 0.002 0.001 HIS G 411 Details of bonding type rmsd covalent geometry : bond 0.00321 (21203) covalent geometry : angle 0.81585 (28828) SS BOND : bond 0.00401 ( 41) SS BOND : angle 1.37767 ( 82) hydrogen bonds : bond 0.04764 ( 526) hydrogen bonds : angle 5.71582 ( 1374) link_ALPHA1-2 : bond 0.00911 ( 11) link_ALPHA1-2 : angle 2.90232 ( 33) link_ALPHA1-3 : bond 0.01175 ( 48) link_ALPHA1-3 : angle 2.10950 ( 144) link_ALPHA1-6 : bond 0.00913 ( 34) link_ALPHA1-6 : angle 1.85781 ( 102) link_BETA1-4 : bond 0.00544 ( 133) link_BETA1-4 : angle 2.04859 ( 399) link_NAG-ASN : bond 0.00371 ( 75) link_NAG-ASN : angle 2.74959 ( 225) *********************** 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 191 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 188 time to evaluate : 0.476 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: A 594 ASN cc_start: 0.9549 (t0) cc_final: 0.9104 (t0) REVERT: A 636 ASP cc_start: 0.8590 (t0) cc_final: 0.8356 (m-30) REVERT: A 653 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8331 (pp30) REVERT: B 530 MET cc_start: 0.8522 (tpp) cc_final: 0.7274 (mmm) REVERT: B 588 LYS cc_start: 0.9485 (tmtt) cc_final: 0.9076 (mtpp) REVERT: B 589 ASP cc_start: 0.9184 (m-30) cc_final: 0.8519 (t70) REVERT: C 530 MET cc_start: 0.7385 (mtt) cc_final: 0.6651 (mmt) REVERT: E 52 LEU cc_start: 0.9384 (mt) cc_final: 0.9164 (mt) REVERT: E 98 ASN cc_start: 0.8346 (t0) cc_final: 0.7343 (t0) REVERT: F 129 MET cc_start: 0.8374 (mtp) cc_final: 0.8062 (mtp) REVERT: F 207 LYS cc_start: 0.8896 (mttm) cc_final: 0.8611 (mmmt) REVERT: F 237 MET cc_start: 0.8802 (ttp) cc_final: 0.8068 (ttm) REVERT: F 251 MET cc_start: 0.8798 (mmm) cc_final: 0.8536 (tpt) REVERT: F 292 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8748 (mt) REVERT: F 294 MET cc_start: 0.8981 (tmm) cc_final: 0.8622 (tmm) REVERT: F 374 MET cc_start: 0.8402 (ppp) cc_final: 0.8087 (ppp) REVERT: F 471 MET cc_start: 0.9348 (ttp) cc_final: 0.9132 (ttp) REVERT: G 98 ASN cc_start: 0.8586 (t0) cc_final: 0.8110 (t0) REVERT: G 161 MET cc_start: 0.8869 (tmm) cc_final: 0.7711 (tmm) REVERT: G 251 MET cc_start: 0.8439 (tmm) cc_final: 0.8236 (tmm) REVERT: G 292 LEU cc_start: 0.8855 (mp) cc_final: 0.8478 (mt) REVERT: G 374 MET cc_start: 0.7882 (tmm) cc_final: 0.7341 (tmm) REVERT: G 471 MET cc_start: 0.8415 (mtp) cc_final: 0.7400 (mtp) REVERT: H 35 HIS cc_start: 0.9069 (m90) cc_final: 0.8868 (m-70) REVERT: H 36 TRP cc_start: 0.8670 (m100) cc_final: 0.7248 (m100) REVERT: H 80 MET cc_start: 0.8292 (ptm) cc_final: 0.7975 (ptm) REVERT: H 100 ARG cc_start: 0.7535 (ttt180) cc_final: 0.7315 (ttp80) REVERT: H 110 HIS cc_start: 0.7268 (m-70) cc_final: 0.6443 (p-80) REVERT: L 32 TYR cc_start: 0.8787 (m-80) cc_final: 0.7917 (m-80) REVERT: L 89 MET cc_start: 0.8878 (tpt) cc_final: 0.8635 (mmm) outliers start: 3 outliers final: 0 residues processed: 190 average time/residue: 0.1346 time to fit residues: 39.6769 Evaluate side-chains 141 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 116 optimal weight: 8.9990 chunk 57 optimal weight: 0.0170 chunk 178 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 392 ASN G 254 GLN G 392 ASN 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 = 0.3514 r_free = 0.3514 target = 0.064256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.047289 restraints weight = 116049.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048888 restraints weight = 62769.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.049901 restraints weight = 43411.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050523 restraints weight = 34919.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.050883 restraints weight = 30728.043| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21545 Z= 0.148 Angle : 0.878 11.312 29813 Z= 0.375 Chirality : 0.050 0.442 4118 Planarity : 0.004 0.055 3172 Dihedral : 13.174 105.537 8339 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.60 % Rotamer: Outliers : 0.00 % Allowed : 2.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.18), residues: 2109 helix: 0.79 (0.26), residues: 393 sheet: -0.83 (0.23), residues: 490 loop : -1.46 (0.18), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 166 TYR 0.022 0.001 TYR B 658 PHE 0.031 0.002 PHE H 100D TRP 0.015 0.001 TRP G 258 HIS 0.003 0.001 HIS F 352 Details of bonding type rmsd covalent geometry : bond 0.00299 (21203) covalent geometry : angle 0.80138 (28828) SS BOND : bond 0.00328 ( 41) SS BOND : angle 1.14349 ( 82) hydrogen bonds : bond 0.04563 ( 526) hydrogen bonds : angle 5.50546 ( 1374) link_ALPHA1-2 : bond 0.00971 ( 11) link_ALPHA1-2 : angle 2.89279 ( 33) link_ALPHA1-3 : bond 0.01174 ( 48) link_ALPHA1-3 : angle 1.90767 ( 144) link_ALPHA1-6 : bond 0.00952 ( 34) link_ALPHA1-6 : angle 1.82363 ( 102) link_BETA1-4 : bond 0.00539 ( 133) link_BETA1-4 : angle 1.92638 ( 399) link_NAG-ASN : bond 0.00426 ( 75) link_NAG-ASN : angle 2.79989 ( 225) *********************** 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 178 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9596 (t0) cc_final: 0.9097 (t0) REVERT: A 636 ASP cc_start: 0.8644 (t0) cc_final: 0.8369 (m-30) REVERT: A 651 ILE cc_start: 0.8288 (mm) cc_final: 0.7977 (mm) REVERT: B 589 ASP cc_start: 0.9202 (m-30) cc_final: 0.8857 (t70) REVERT: C 530 MET cc_start: 0.7390 (mtt) cc_final: 0.6605 (mmt) REVERT: C 576 LEU cc_start: 0.8672 (mt) cc_final: 0.8265 (mt) REVERT: C 586 TYR cc_start: 0.9243 (t80) cc_final: 0.8744 (t80) REVERT: E 52 LEU cc_start: 0.9381 (mt) cc_final: 0.9050 (mt) REVERT: E 98 ASN cc_start: 0.8175 (t0) cc_final: 0.7448 (t0) REVERT: E 251 MET cc_start: 0.9001 (ttp) cc_final: 0.8303 (tmm) REVERT: E 377 ASN cc_start: 0.8422 (t0) cc_final: 0.8013 (m-40) REVERT: F 129 MET cc_start: 0.8440 (mtp) cc_final: 0.8123 (mtp) REVERT: F 207 LYS cc_start: 0.8926 (mttm) cc_final: 0.8671 (mmmt) REVERT: F 237 MET cc_start: 0.8727 (ttp) cc_final: 0.8039 (ttm) REVERT: F 251 MET cc_start: 0.8834 (mmm) cc_final: 0.8632 (tpt) REVERT: F 294 MET cc_start: 0.8924 (tmm) cc_final: 0.8536 (tmm) REVERT: F 310 MET cc_start: 0.8550 (ppp) cc_final: 0.8079 (ppp) REVERT: F 374 MET cc_start: 0.8494 (ppp) cc_final: 0.8129 (ppp) REVERT: F 471 MET cc_start: 0.9276 (ttp) cc_final: 0.8846 (ttp) REVERT: G 98 ASN cc_start: 0.8503 (t0) cc_final: 0.8100 (t0) REVERT: G 161 MET cc_start: 0.8849 (tmm) cc_final: 0.8436 (tmm) REVERT: G 251 MET cc_start: 0.8503 (tmm) cc_final: 0.8283 (tmm) REVERT: G 292 LEU cc_start: 0.9077 (mp) cc_final: 0.8401 (mt) REVERT: H 35 HIS cc_start: 0.9103 (m90) cc_final: 0.8611 (m-70) REVERT: H 36 TRP cc_start: 0.8733 (m100) cc_final: 0.7528 (m100) REVERT: H 48 MET cc_start: 0.6543 (mtp) cc_final: 0.5773 (mtp) REVERT: H 80 MET cc_start: 0.8386 (ptm) cc_final: 0.8024 (ptm) REVERT: H 110 HIS cc_start: 0.7281 (m-70) cc_final: 0.6497 (p-80) REVERT: L 32 TYR cc_start: 0.8793 (m-80) cc_final: 0.7919 (m-80) REVERT: L 89 MET cc_start: 0.8761 (tpt) cc_final: 0.8501 (mmm) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.1278 time to fit residues: 35.6671 Evaluate side-chains 135 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 200 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN C 551 GLN E 202 GLN E 410 GLN F 208 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.062658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045353 restraints weight = 121470.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046830 restraints weight = 68321.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.047757 restraints weight = 48912.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048304 restraints weight = 40408.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.048635 restraints weight = 36246.531| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21545 Z= 0.212 Angle : 0.918 9.925 29813 Z= 0.399 Chirality : 0.050 0.441 4118 Planarity : 0.004 0.050 3172 Dihedral : 12.382 104.751 8339 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.68 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.18), residues: 2109 helix: 0.72 (0.26), residues: 395 sheet: -0.88 (0.24), residues: 439 loop : -1.54 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 439 TYR 0.018 0.002 TYR B 658 PHE 0.021 0.002 PHE H 29 TRP 0.022 0.002 TRP A 623 HIS 0.004 0.001 HIS E 428 Details of bonding type rmsd covalent geometry : bond 0.00448 (21203) covalent geometry : angle 0.83920 (28828) SS BOND : bond 0.00326 ( 41) SS BOND : angle 1.50569 ( 82) hydrogen bonds : bond 0.04682 ( 526) hydrogen bonds : angle 5.55965 ( 1374) link_ALPHA1-2 : bond 0.00862 ( 11) link_ALPHA1-2 : angle 2.87642 ( 33) link_ALPHA1-3 : bond 0.01080 ( 48) link_ALPHA1-3 : angle 2.04025 ( 144) link_ALPHA1-6 : bond 0.00939 ( 34) link_ALPHA1-6 : angle 2.00028 ( 102) link_BETA1-4 : bond 0.00538 ( 133) link_BETA1-4 : angle 1.95505 ( 399) link_NAG-ASN : bond 0.00482 ( 75) link_NAG-ASN : angle 2.87156 ( 225) *********************** 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 165 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.763 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: 0.9617 (t0) cc_final: 0.9175 (t0) REVERT: A 636 ASP cc_start: 0.8827 (t0) cc_final: 0.8346 (m-30) REVERT: A 639 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8700 (mm-30) REVERT: B 530 MET cc_start: 0.8669 (tpp) cc_final: 0.7360 (mmm) REVERT: B 574 LYS cc_start: 0.8496 (tppt) cc_final: 0.8261 (tppp) REVERT: B 596 TRP cc_start: 0.9233 (m-10) cc_final: 0.8514 (m-10) REVERT: C 530 MET cc_start: 0.7562 (mtt) cc_final: 0.6750 (mmt) REVERT: E 52 LEU cc_start: 0.9362 (mt) cc_final: 0.9137 (mt) REVERT: E 98 ASN cc_start: 0.8472 (t0) cc_final: 0.7756 (t0) REVERT: E 251 MET cc_start: 0.8979 (ttp) cc_final: 0.8225 (tmm) REVERT: F 69 TRP cc_start: 0.7376 (p90) cc_final: 0.6991 (p90) REVERT: F 129 MET cc_start: 0.8572 (mtp) cc_final: 0.8291 (mtp) REVERT: F 161 MET cc_start: 0.8998 (tpp) cc_final: 0.8586 (tpp) REVERT: F 207 LYS cc_start: 0.8954 (mttm) cc_final: 0.8723 (mmmt) REVERT: F 237 MET cc_start: 0.8765 (ttp) cc_final: 0.8536 (tpp) REVERT: F 294 MET cc_start: 0.8923 (tmm) cc_final: 0.8526 (tmm) REVERT: F 310 MET cc_start: 0.8584 (ppp) cc_final: 0.8332 (ppp) REVERT: F 374 MET cc_start: 0.8632 (ppp) cc_final: 0.8162 (ppp) REVERT: G 98 ASN cc_start: 0.8754 (t0) cc_final: 0.8306 (t0) REVERT: G 161 MET cc_start: 0.8837 (tmm) cc_final: 0.8544 (tmm) REVERT: G 251 MET cc_start: 0.8498 (tmm) cc_final: 0.8226 (tmm) REVERT: G 471 MET cc_start: 0.8827 (mpp) cc_final: 0.8274 (mpp) REVERT: H 48 MET cc_start: 0.6657 (mtp) cc_final: 0.6040 (mtp) REVERT: H 80 MET cc_start: 0.8395 (ptm) cc_final: 0.7934 (ptm) REVERT: L 32 TYR cc_start: 0.8967 (m-80) cc_final: 0.8116 (m-80) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1238 time to fit residues: 32.7762 Evaluate side-chains 119 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 159 optimal weight: 7.9990 chunk 136 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 653 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 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.063273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.046309 restraints weight = 116965.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047856 restraints weight = 63340.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048841 restraints weight = 44117.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.049445 restraints weight = 35674.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.049779 restraints weight = 31472.183| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21545 Z= 0.154 Angle : 0.871 11.468 29813 Z= 0.374 Chirality : 0.050 0.439 4118 Planarity : 0.004 0.051 3172 Dihedral : 11.754 103.451 8339 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.56 % Rotamer: Outliers : 0.05 % Allowed : 1.70 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.18), residues: 2109 helix: 0.64 (0.26), residues: 406 sheet: -0.93 (0.23), residues: 502 loop : -1.58 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 46 TYR 0.024 0.001 TYR B 658 PHE 0.018 0.002 PHE H 29 TRP 0.012 0.001 TRP F 258 HIS 0.005 0.001 HIS E 428 Details of bonding type rmsd covalent geometry : bond 0.00322 (21203) covalent geometry : angle 0.79279 (28828) SS BOND : bond 0.00325 ( 41) SS BOND : angle 1.33648 ( 82) hydrogen bonds : bond 0.04346 ( 526) hydrogen bonds : angle 5.44222 ( 1374) link_ALPHA1-2 : bond 0.00964 ( 11) link_ALPHA1-2 : angle 2.78314 ( 33) link_ALPHA1-3 : bond 0.01103 ( 48) link_ALPHA1-3 : angle 1.87506 ( 144) link_ALPHA1-6 : bond 0.00986 ( 34) link_ALPHA1-6 : angle 1.86145 ( 102) link_BETA1-4 : bond 0.00522 ( 133) link_BETA1-4 : angle 1.84877 ( 399) link_NAG-ASN : bond 0.00373 ( 75) link_NAG-ASN : angle 2.87768 ( 225) *********************** 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 168 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.741 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 594 ASN cc_start: 0.9602 (t0) cc_final: 0.9127 (t0) REVERT: A 636 ASP cc_start: 0.8796 (t0) cc_final: 0.8380 (m-30) REVERT: A 639 GLU cc_start: 0.9230 (mm-30) cc_final: 0.8708 (mm-30) REVERT: B 530 MET cc_start: 0.8588 (tpp) cc_final: 0.7404 (mmm) REVERT: B 574 LYS cc_start: 0.8415 (tppt) cc_final: 0.8203 (tppp) REVERT: B 588 LYS cc_start: 0.9488 (tmtt) cc_final: 0.9138 (mtpp) REVERT: B 589 ASP cc_start: 0.9180 (m-30) cc_final: 0.8855 (m-30) REVERT: C 530 MET cc_start: 0.7415 (mtt) cc_final: 0.6686 (mmt) REVERT: C 624 ASN cc_start: 0.9395 (m-40) cc_final: 0.9048 (t0) REVERT: E 52 LEU cc_start: 0.9300 (mt) cc_final: 0.9062 (mt) REVERT: E 98 ASN cc_start: 0.8355 (t0) cc_final: 0.7683 (t0) REVERT: E 251 MET cc_start: 0.9005 (ttp) cc_final: 0.8321 (tmm) REVERT: E 377 ASN cc_start: 0.8368 (t0) cc_final: 0.7859 (m-40) REVERT: F 129 MET cc_start: 0.8368 (mtp) cc_final: 0.7998 (mtp) REVERT: F 207 LYS cc_start: 0.8896 (mttm) cc_final: 0.8626 (mmmt) REVERT: F 237 MET cc_start: 0.8703 (ttp) cc_final: 0.8032 (ttm) REVERT: F 294 MET cc_start: 0.8943 (tmm) cc_final: 0.8539 (tmm) REVERT: F 310 MET cc_start: 0.8602 (ppp) cc_final: 0.8381 (ppp) REVERT: F 374 MET cc_start: 0.8594 (ppp) cc_final: 0.8277 (ppp) REVERT: F 471 MET cc_start: 0.9249 (ttp) cc_final: 0.8871 (ttp) REVERT: G 98 ASN cc_start: 0.8615 (t0) cc_final: 0.8177 (t0) REVERT: G 161 MET cc_start: 0.9014 (tmm) cc_final: 0.8628 (tmm) REVERT: G 251 MET cc_start: 0.8520 (tmm) cc_final: 0.8208 (tmm) REVERT: G 471 MET cc_start: 0.8764 (mpp) cc_final: 0.8372 (mpp) REVERT: H 80 MET cc_start: 0.8299 (ptm) cc_final: 0.7846 (ptm) REVERT: H 110 HIS cc_start: 0.7430 (m90) cc_final: 0.7095 (p-80) REVERT: L 32 TYR cc_start: 0.8928 (m-80) cc_final: 0.8105 (m-80) REVERT: L 89 MET cc_start: 0.8628 (mmm) cc_final: 0.8340 (mmm) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.1324 time to fit residues: 35.4197 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 : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 187 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 135 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN E 202 GLN ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 410 GLN G 428 HIS L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.062628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.045508 restraints weight = 117990.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047022 restraints weight = 64245.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.047987 restraints weight = 45044.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.048568 restraints weight = 36578.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.048916 restraints weight = 32448.305| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21545 Z= 0.181 Angle : 0.884 10.480 29813 Z= 0.385 Chirality : 0.049 0.435 4118 Planarity : 0.004 0.064 3172 Dihedral : 11.290 102.083 8339 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.01 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.18), residues: 2109 helix: 0.81 (0.26), residues: 393 sheet: -0.92 (0.23), residues: 502 loop : -1.46 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 268 TYR 0.032 0.002 TYR B 658 PHE 0.019 0.002 PHE C 600 TRP 0.015 0.001 TRP E 258 HIS 0.005 0.001 HIS G 274 Details of bonding type rmsd covalent geometry : bond 0.00381 (21203) covalent geometry : angle 0.80735 (28828) SS BOND : bond 0.00312 ( 41) SS BOND : angle 1.32688 ( 82) hydrogen bonds : bond 0.04316 ( 526) hydrogen bonds : angle 5.53131 ( 1374) link_ALPHA1-2 : bond 0.00857 ( 11) link_ALPHA1-2 : angle 2.77092 ( 33) link_ALPHA1-3 : bond 0.01044 ( 48) link_ALPHA1-3 : angle 1.88414 ( 144) link_ALPHA1-6 : bond 0.01006 ( 34) link_ALPHA1-6 : angle 1.88370 ( 102) link_BETA1-4 : bond 0.00531 ( 133) link_BETA1-4 : angle 1.85179 ( 399) link_NAG-ASN : bond 0.00414 ( 75) link_NAG-ASN : angle 2.86329 ( 225) *********************** 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 161 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.680 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: 0.9624 (t0) cc_final: 0.9203 (t0) REVERT: A 636 ASP cc_start: 0.8817 (t0) cc_final: 0.8342 (m-30) REVERT: A 639 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8690 (mm-30) REVERT: C 530 MET cc_start: 0.7354 (mtt) cc_final: 0.6660 (mmt) REVERT: E 52 LEU cc_start: 0.9266 (mt) cc_final: 0.9027 (mt) REVERT: E 98 ASN cc_start: 0.8357 (t0) cc_final: 0.7740 (t0) REVERT: E 129 MET cc_start: 0.8526 (mtt) cc_final: 0.8311 (mtp) REVERT: E 251 MET cc_start: 0.9019 (ttp) cc_final: 0.8353 (tmm) REVERT: E 377 ASN cc_start: 0.8274 (t0) cc_final: 0.7814 (m-40) REVERT: E 471 MET cc_start: 0.9249 (ttp) cc_final: 0.9033 (ttp) REVERT: F 69 TRP cc_start: 0.7350 (p90) cc_final: 0.6941 (p90) REVERT: F 129 MET cc_start: 0.8442 (mtp) cc_final: 0.8115 (mtp) REVERT: F 194 ASN cc_start: 0.9021 (t0) cc_final: 0.8815 (t0) REVERT: F 207 LYS cc_start: 0.8876 (mttm) cc_final: 0.8609 (mmmt) REVERT: F 237 MET cc_start: 0.8764 (ttp) cc_final: 0.8114 (ttm) REVERT: F 294 MET cc_start: 0.8981 (tmm) cc_final: 0.8587 (tmm) REVERT: F 374 MET cc_start: 0.8678 (ppp) cc_final: 0.8276 (ppp) REVERT: F 471 MET cc_start: 0.9250 (ttp) cc_final: 0.8820 (ttp) REVERT: G 98 ASN cc_start: 0.8720 (t0) cc_final: 0.8305 (t0) REVERT: G 161 MET cc_start: 0.8996 (tmm) cc_final: 0.8606 (tmm) REVERT: G 251 MET cc_start: 0.8478 (tmm) cc_final: 0.8171 (tmm) REVERT: G 374 MET cc_start: 0.8156 (tmm) cc_final: 0.7929 (tmm) REVERT: G 387 MET cc_start: 0.9514 (ptm) cc_final: 0.9249 (ppp) REVERT: G 471 MET cc_start: 0.8814 (mpp) cc_final: 0.8424 (mpp) REVERT: H 80 MET cc_start: 0.8376 (ptm) cc_final: 0.7998 (ptm) REVERT: H 110 HIS cc_start: 0.7316 (m90) cc_final: 0.7016 (p-80) REVERT: L 32 TYR cc_start: 0.8968 (m-80) cc_final: 0.8149 (m-80) REVERT: L 89 MET cc_start: 0.8695 (mmm) cc_final: 0.8394 (mmm) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1236 time to fit residues: 32.6476 Evaluate side-chains 118 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 74 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 9 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 199 optimal weight: 30.0000 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- 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 653 GLN 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 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.064241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.047398 restraints weight = 119396.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.048882 restraints weight = 66353.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.049825 restraints weight = 47217.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.050391 restraints weight = 38771.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.050695 restraints weight = 34637.286| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4851 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 : 0.874 16.801 29813 Z= 0.381 Chirality : 0.049 0.427 4118 Planarity : 0.004 0.052 3172 Dihedral : 10.673 100.511 8339 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.40 % Favored : 92.51 % 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 : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.18), residues: 2109 helix: 0.58 (0.26), residues: 393 sheet: -0.78 (0.24), residues: 445 loop : -1.48 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 249 TYR 0.024 0.001 TYR B 658 PHE 0.019 0.002 PHE C 600 TRP 0.015 0.001 TRP E 258 HIS 0.004 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00299 (21203) covalent geometry : angle 0.80098 (28828) SS BOND : bond 0.00336 ( 41) SS BOND : angle 1.05970 ( 82) hydrogen bonds : bond 0.04199 ( 526) hydrogen bonds : angle 5.46941 ( 1374) link_ALPHA1-2 : bond 0.00929 ( 11) link_ALPHA1-2 : angle 2.71006 ( 33) link_ALPHA1-3 : bond 0.01072 ( 48) link_ALPHA1-3 : angle 1.76469 ( 144) link_ALPHA1-6 : bond 0.01055 ( 34) link_ALPHA1-6 : angle 1.72572 ( 102) link_BETA1-4 : bond 0.00533 ( 133) link_BETA1-4 : angle 1.79813 ( 399) link_NAG-ASN : bond 0.00355 ( 75) link_NAG-ASN : angle 2.89101 ( 225) *********************** 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 167 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9613 (t0) cc_final: 0.9172 (t0) REVERT: A 636 ASP cc_start: 0.8801 (t0) cc_final: 0.8321 (m-30) REVERT: A 639 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8630 (mm-30) REVERT: B 530 MET cc_start: 0.8541 (tpp) cc_final: 0.7584 (mmm) REVERT: B 588 LYS cc_start: 0.9486 (tmtt) cc_final: 0.9159 (mtpp) REVERT: B 589 ASP cc_start: 0.9212 (m-30) cc_final: 0.8917 (m-30) REVERT: C 530 MET cc_start: 0.7255 (mtt) cc_final: 0.6468 (mmt) REVERT: C 542 ARG cc_start: 0.8008 (ptp90) cc_final: 0.7241 (ptp90) REVERT: E 52 LEU cc_start: 0.9270 (mt) cc_final: 0.8950 (mt) REVERT: E 98 ASN cc_start: 0.8121 (t0) cc_final: 0.7587 (t0) REVERT: E 251 MET cc_start: 0.8987 (ttp) cc_final: 0.8199 (tmm) REVERT: E 377 ASN cc_start: 0.8253 (t0) cc_final: 0.7825 (m-40) REVERT: F 129 MET cc_start: 0.8344 (mtp) cc_final: 0.7395 (mtp) REVERT: F 194 ASN cc_start: 0.8992 (t0) cc_final: 0.8780 (t0) REVERT: F 207 LYS cc_start: 0.8857 (mttm) cc_final: 0.8534 (mmmt) REVERT: F 237 MET cc_start: 0.8737 (ttp) cc_final: 0.8147 (ttm) REVERT: F 294 MET cc_start: 0.8958 (tmm) cc_final: 0.8546 (tmm) REVERT: F 310 MET cc_start: 0.8538 (ppp) cc_final: 0.8016 (ppp) REVERT: F 374 MET cc_start: 0.8649 (ppp) cc_final: 0.8263 (ppp) REVERT: F 471 MET cc_start: 0.9271 (ttp) cc_final: 0.8748 (ttp) REVERT: G 98 ASN cc_start: 0.8471 (t0) cc_final: 0.8050 (t0) REVERT: G 161 MET cc_start: 0.8988 (tmm) cc_final: 0.8639 (tmm) REVERT: G 251 MET cc_start: 0.8500 (tmm) cc_final: 0.8249 (tmm) REVERT: G 292 LEU cc_start: 0.9115 (mp) cc_final: 0.8515 (mt) REVERT: G 387 MET cc_start: 0.9511 (ptm) cc_final: 0.9210 (ppp) REVERT: G 471 MET cc_start: 0.8886 (mpp) cc_final: 0.8439 (mpp) REVERT: H 37 VAL cc_start: 0.9202 (t) cc_final: 0.8916 (p) REVERT: H 80 MET cc_start: 0.8230 (ptm) cc_final: 0.7900 (ptm) REVERT: H 100 LEU cc_start: 0.9386 (tt) cc_final: 0.9164 (tt) REVERT: L 32 TYR cc_start: 0.8885 (m-80) cc_final: 0.8067 (m-80) REVERT: L 89 MET cc_start: 0.8657 (mmm) cc_final: 0.8374 (mmm) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1235 time to fit residues: 33.1770 Evaluate side-chains 126 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 94 optimal weight: 0.2980 chunk 163 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 202 optimal weight: 0.0170 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 overall best weight: 1.0420 ------------------------------------------------------------------------------- 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 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN B 629 GLN 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 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.064236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.047462 restraints weight = 120606.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.048961 restraints weight = 67101.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.049886 restraints weight = 47572.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.050466 restraints weight = 39063.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.050759 restraints weight = 34805.824| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.5007 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= 0.145 Angle : 0.859 16.490 29813 Z= 0.373 Chirality : 0.048 0.416 4118 Planarity : 0.004 0.052 3172 Dihedral : 10.146 100.135 8339 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.49 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.18), residues: 2109 helix: 0.59 (0.27), residues: 393 sheet: -0.78 (0.23), residues: 497 loop : -1.43 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 268 TYR 0.025 0.001 TYR B 658 PHE 0.021 0.002 PHE C 600 TRP 0.016 0.001 TRP F 69 HIS 0.003 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00297 (21203) covalent geometry : angle 0.78786 (28828) SS BOND : bond 0.00290 ( 41) SS BOND : angle 1.28319 ( 82) hydrogen bonds : bond 0.03974 ( 526) hydrogen bonds : angle 5.40816 ( 1374) link_ALPHA1-2 : bond 0.00864 ( 11) link_ALPHA1-2 : angle 2.65693 ( 33) link_ALPHA1-3 : bond 0.01017 ( 48) link_ALPHA1-3 : angle 1.74392 ( 144) link_ALPHA1-6 : bond 0.01048 ( 34) link_ALPHA1-6 : angle 1.68234 ( 102) link_BETA1-4 : bond 0.00529 ( 133) link_BETA1-4 : angle 1.80055 ( 399) link_NAG-ASN : bond 0.00329 ( 75) link_NAG-ASN : angle 2.74735 ( 225) ********************** 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 165 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.711 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: 0.9601 (t0) cc_final: 0.9149 (t0) REVERT: A 636 ASP cc_start: 0.8799 (t0) cc_final: 0.8315 (m-30) REVERT: A 639 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8634 (mm-30) REVERT: B 548 ILE cc_start: 0.9415 (mm) cc_final: 0.9192 (tp) REVERT: B 588 LYS cc_start: 0.9484 (tmtt) cc_final: 0.9154 (mtpp) REVERT: B 589 ASP cc_start: 0.9215 (m-30) cc_final: 0.8934 (m-30) REVERT: B 651 ILE cc_start: 0.8846 (pt) cc_final: 0.8486 (pt) REVERT: C 530 MET cc_start: 0.7195 (mtt) cc_final: 0.6428 (mmt) REVERT: C 538 THR cc_start: 0.9156 (m) cc_final: 0.8915 (m) REVERT: E 52 LEU cc_start: 0.9250 (mt) cc_final: 0.8945 (mt) REVERT: E 98 ASN cc_start: 0.8051 (t0) cc_final: 0.7180 (t0) REVERT: E 251 MET cc_start: 0.8979 (ttp) cc_final: 0.8108 (tmm) REVERT: E 377 ASN cc_start: 0.8190 (t0) cc_final: 0.7827 (m-40) REVERT: F 69 TRP cc_start: 0.7240 (p90) cc_final: 0.6815 (p90) REVERT: F 129 MET cc_start: 0.8361 (mtp) cc_final: 0.7332 (mtp) REVERT: F 194 ASN cc_start: 0.9041 (t0) cc_final: 0.8817 (t0) REVERT: F 207 LYS cc_start: 0.8846 (mttm) cc_final: 0.8550 (mmmt) REVERT: F 237 MET cc_start: 0.8696 (ttp) cc_final: 0.8123 (ttm) REVERT: F 251 MET cc_start: 0.9031 (tpp) cc_final: 0.8711 (tmm) REVERT: F 294 MET cc_start: 0.8950 (tmm) cc_final: 0.8579 (tmm) REVERT: F 310 MET cc_start: 0.8445 (ppp) cc_final: 0.7742 (ppp) REVERT: F 374 MET cc_start: 0.8670 (ppp) cc_final: 0.8260 (ppp) REVERT: F 471 MET cc_start: 0.9251 (ttp) cc_final: 0.8638 (ttp) REVERT: G 98 ASN cc_start: 0.8490 (t0) cc_final: 0.8092 (t0) REVERT: G 161 MET cc_start: 0.8982 (tmm) cc_final: 0.8674 (tmm) REVERT: G 237 MET cc_start: 0.8391 (ppp) cc_final: 0.8126 (tmm) REVERT: G 387 MET cc_start: 0.9532 (ptm) cc_final: 0.8974 (ppp) REVERT: G 471 MET cc_start: 0.9042 (mpp) cc_final: 0.8310 (mtm) REVERT: H 37 VAL cc_start: 0.9235 (t) cc_final: 0.9028 (t) REVERT: H 80 MET cc_start: 0.8226 (ptm) cc_final: 0.7899 (ptm) REVERT: H 100 LEU cc_start: 0.9386 (tt) cc_final: 0.9121 (tt) REVERT: H 110 HIS cc_start: 0.7355 (m90) cc_final: 0.7066 (m-70) REVERT: L 32 TYR cc_start: 0.8912 (m-80) cc_final: 0.8105 (m-80) REVERT: L 89 MET cc_start: 0.8677 (mmm) cc_final: 0.8402 (mmm) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1259 time to fit residues: 33.5890 Evaluate side-chains 128 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 179 optimal weight: 0.0570 chunk 147 optimal weight: 0.0770 chunk 204 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.2260 ------------------------------------------------------------------------------- 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 575 ASN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 428 HIS L 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.063812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.046884 restraints weight = 120783.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048388 restraints weight = 67334.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.049329 restraints weight = 47819.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.049877 restraints weight = 39209.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.050113 restraints weight = 35079.262| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21545 Z= 0.144 Angle : 0.847 12.600 29813 Z= 0.371 Chirality : 0.047 0.415 4118 Planarity : 0.004 0.092 3172 Dihedral : 9.850 100.347 8339 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.40 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.18), residues: 2109 helix: 0.49 (0.26), residues: 407 sheet: -0.79 (0.23), residues: 502 loop : -1.46 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 633 TYR 0.033 0.001 TYR B 658 PHE 0.021 0.001 PHE C 600 TRP 0.016 0.001 TRP E 258 HIS 0.003 0.001 HIS F 352 Details of bonding type rmsd covalent geometry : bond 0.00297 (21203) covalent geometry : angle 0.77841 (28828) SS BOND : bond 0.00296 ( 41) SS BOND : angle 1.25177 ( 82) hydrogen bonds : bond 0.03937 ( 526) hydrogen bonds : angle 5.38602 ( 1374) link_ALPHA1-2 : bond 0.00831 ( 11) link_ALPHA1-2 : angle 2.62123 ( 33) link_ALPHA1-3 : bond 0.00990 ( 48) link_ALPHA1-3 : angle 1.74273 ( 144) link_ALPHA1-6 : bond 0.01020 ( 34) link_ALPHA1-6 : angle 1.65062 ( 102) link_BETA1-4 : bond 0.00528 ( 133) link_BETA1-4 : angle 1.78226 ( 399) link_NAG-ASN : bond 0.00327 ( 75) link_NAG-ASN : angle 2.67228 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2636.16 seconds wall clock time: 47 minutes 9.26 seconds (2829.26 seconds total)