Starting phenix.real_space_refine on Sat Jul 4 13:09:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dvd_27735/07_2026/8dvd_27735.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvd_27735/07_2026/8dvd_27735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dvd_27735/07_2026/8dvd_27735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvd_27735/07_2026/8dvd_27735.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dvd_27735/07_2026/8dvd_27735.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dvd_27735/07_2026/8dvd_27735.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dvd_27735/07_2026/8dvd_27735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvd_27735/07_2026/8dvd_27735.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 5.51, 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: 3.33 Conformation dependent library (CDL) restraints added in 598.9 milliseconds 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: 0.53 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: 3.88 Time building geometry restraints manager: 3.84 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 - 16.65: 9149 16.65 - 33.30: 1002 33.30 - 49.95: 230 49.95 - 66.60: 43 66.60 - 83.25: 19 Dihedral angle restraints: 10443 sinusoidal: 4228 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 10440 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.610 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 14.375 83.254 6310 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 are 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/Z covalent geometry : bond 0.00670 / 0.33 (21203) covalent geometry : angle 1.07069 / 0.42 (28828) SS BOND : bond 0.00272 / 0.15 ( 41) SS BOND : angle 1.80948 / 1.62 ( 82) hydrogen bonds : bond 0.28177 / 18.77 ( 526) hydrogen bonds : angle 8.81945 / 6.38 ( 1374) link_ALPHA1-2 : bond 0.00532 / 0.39 ( 11) link_ALPHA1-2 : angle 2.46328 / 1.66 ( 33) link_ALPHA1-3 : bond 0.00568 / 0.34 ( 48) link_ALPHA1-3 : angle 1.92684 / 1.36 ( 144) link_ALPHA1-6 : bond 0.00517 / 0.34 ( 34) link_ALPHA1-6 : angle 1.65619 / 1.22 ( 102) link_BETA1-4 : bond 0.00564 / 0.38 ( 133) link_BETA1-4 : angle 2.10009 / 1.55 ( 399) link_NAG-ASN : bond 0.01791 / 1.42 ( 75) link_NAG-ASN : angle 3.18598 / 2.01 ( 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 : 0.626 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9198 (t0) cc_final: 0.8971 (t0) REVERT: A 651 ILE cc_start: 0.8629 (mt) cc_final: 0.7631 (mm) REVERT: G 161 MET cc_start: 0.8334 (tmm) cc_final: 0.7946 (tmm) REVERT: G 354 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7563 (p0) REVERT: H 33 ASP cc_start: 0.8662 (m-30) cc_final: 0.8284 (t0) REVERT: H 110 HIS cc_start: 0.6301 (m-70) cc_final: 0.5834 (p-80) REVERT: L 32 TYR cc_start: 0.8359 (m-80) cc_final: 0.8090 (m-80) outliers start: 13 outliers final: 6 residues processed: 363 average time/residue: 0.1564 time to fit residues: 85.1959 Evaluate side-chains 167 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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: 0.0670 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN B 602 GLN B 629 GLN E 103 GLN E 254 GLN E 419 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 = 0.3579 r_free = 0.3579 target = 0.066498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.049582 restraints weight = 114126.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.051214 restraints weight = 61540.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.052272 restraints weight = 42475.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.052929 restraints weight = 34008.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.053284 restraints weight = 29816.582| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21545 Z= 0.177 Angle : 0.937 12.247 29813 Z= 0.410 Chirality : 0.047 0.525 4118 Planarity : 0.005 0.065 3172 Dihedral : 4.995 30.041 2307 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.92 % Favored : 92.98 % Rotamer: Outliers : 0.27 % Allowed : 4.53 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.18), residues: 2109 helix: 1.15 (0.26), residues: 371 sheet: -0.62 (0.22), residues: 571 loop : -1.36 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 633 TYR 0.019 0.001 TYR B 658 PHE 0.031 0.002 PHE H 100D TRP 0.028 0.001 TRP H 108 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (21203) covalent geometry : angle 0.84070 / 0.39 (28828) SS BOND : bond 0.00289 / 0.18 ( 41) SS BOND : angle 1.13757 / 0.97 ( 82) hydrogen bonds : bond 0.07040 / 4.70 ( 526) hydrogen bonds : angle 6.70608 / 4.92 ( 1374) link_ALPHA1-2 : bond 0.00829 / 0.55 ( 11) link_ALPHA1-2 : angle 2.82392 / 1.91 ( 33) link_ALPHA1-3 : bond 0.00620 / 0.42 ( 48) link_ALPHA1-3 : angle 1.89908 / 1.33 ( 144) link_ALPHA1-6 : bond 0.00493 / 0.34 ( 34) link_ALPHA1-6 : angle 1.60963 / 1.19 ( 102) link_BETA1-4 : bond 0.00586 / 0.40 ( 133) link_BETA1-4 : angle 2.19229 / 1.58 ( 399) link_NAG-ASN : bond 0.00555 / 0.34 ( 75) link_NAG-ASN : angle 3.47394 / 2.25 ( 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 223 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 ASN cc_start: 0.9538 (t0) cc_final: 0.9124 (t0) REVERT: A 630 GLU cc_start: 0.9477 (pt0) cc_final: 0.9238 (pt0) REVERT: B 640 GLU cc_start: 0.8396 (pm20) cc_final: 0.7946 (pm20) REVERT: C 576 LEU cc_start: 0.8580 (mm) cc_final: 0.7664 (mm) REVERT: C 585 LYS cc_start: 0.9140 (tptp) cc_final: 0.8709 (tptp) REVERT: E 98 ASN cc_start: 0.8616 (t0) cc_final: 0.7697 (t0) REVERT: E 106 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7999 (tm-30) REVERT: E 471 MET cc_start: 0.8781 (mmm) cc_final: 0.8542 (mmm) REVERT: F 294 MET cc_start: 0.8891 (tmm) cc_final: 0.8649 (tmm) REVERT: G 98 ASN cc_start: 0.8735 (t0) cc_final: 0.8072 (t0) REVERT: G 161 MET cc_start: 0.8791 (tmm) cc_final: 0.7619 (tmm) REVERT: G 374 MET cc_start: 0.7905 (tmm) cc_final: 0.7545 (tmm) REVERT: H 33 ASP cc_start: 0.9056 (m-30) cc_final: 0.8805 (t0) REVERT: H 36 TRP cc_start: 0.8750 (m100) cc_final: 0.7402 (m100) REVERT: H 46 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8726 (tt0) REVERT: H 80 MET cc_start: 0.8053 (ptm) cc_final: 0.7452 (ptm) REVERT: H 100 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7486 (tp30) REVERT: H 110 HIS cc_start: 0.7693 (m-70) cc_final: 0.6711 (p-80) REVERT: L 32 TYR cc_start: 0.8769 (m-80) cc_final: 0.7958 (m-80) outliers start: 5 outliers final: 1 residues processed: 222 average time/residue: 0.1425 time to fit residues: 49.3759 Evaluate side-chains 151 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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: 9.9990 chunk 195 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 187 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN C 540 GLN C 551 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 HIS E 428 HIS ** F 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN G 254 GLN G 411 HIS L 27 HIS L 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.062809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.045832 restraints weight = 119190.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.047297 restraints weight = 66418.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048236 restraints weight = 47152.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.048806 restraints weight = 38581.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.049118 restraints weight = 34366.186| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 21545 Z= 0.281 Angle : 0.960 12.212 29813 Z= 0.431 Chirality : 0.046 0.387 4118 Planarity : 0.005 0.056 3172 Dihedral : 5.477 36.039 2307 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.08 % Rotamer: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % 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 are not related in a simple way. whole: -1.37 (0.18), residues: 2109 helix: 0.74 (0.26), residues: 389 sheet: -0.94 (0.22), residues: 578 loop : -1.48 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 579 TYR 0.016 0.002 TYR G 270 PHE 0.028 0.002 PHE H 100D TRP 0.020 0.002 TRP F 258 HIS 0.006 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.28 (21203) covalent geometry : angle 0.88420 / 0.42 (28828) SS BOND : bond 0.00477 / 0.27 ( 41) SS BOND : angle 1.82903 / 1.43 ( 82) hydrogen bonds : bond 0.05841 / 3.93 ( 526) hydrogen bonds : angle 6.14875 / 4.52 ( 1374) link_ALPHA1-2 : bond 0.00447 / 0.26 ( 11) link_ALPHA1-2 : angle 2.73028 / 1.87 ( 33) link_ALPHA1-3 : bond 0.00616 / 0.39 ( 48) link_ALPHA1-3 : angle 1.86827 / 1.31 ( 144) link_ALPHA1-6 : bond 0.00435 / 0.29 ( 34) link_ALPHA1-6 : angle 1.73434 / 1.28 ( 102) link_BETA1-4 : bond 0.00550 / 0.38 ( 133) link_BETA1-4 : angle 1.98754 / 1.44 ( 399) link_NAG-ASN : bond 0.00618 / 0.40 ( 75) link_NAG-ASN : angle 3.01682 / 2.11 ( 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 185 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.761 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 576 LEU cc_start: 0.8461 (mt) cc_final: 0.8259 (mt) REVERT: A 594 ASN cc_start: 0.9602 (t0) cc_final: 0.9169 (t0) REVERT: B 589 ASP cc_start: 0.9222 (m-30) cc_final: 0.8835 (t70) REVERT: C 596 TRP cc_start: 0.8886 (m-10) cc_final: 0.8246 (m-10) REVERT: E 52 LEU cc_start: 0.9397 (mt) cc_final: 0.9162 (mt) REVERT: E 98 ASN cc_start: 0.8682 (t0) cc_final: 0.7772 (t0) REVERT: E 106 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8037 (tm-30) REVERT: E 149 ILE cc_start: 0.9520 (tt) cc_final: 0.9262 (mm) REVERT: E 294 MET cc_start: 0.8514 (tmm) cc_final: 0.8109 (tmm) REVERT: E 471 MET cc_start: 0.8865 (mmm) cc_final: 0.8500 (mmm) REVERT: F 129 MET cc_start: 0.8811 (mtp) cc_final: 0.8477 (mtp) REVERT: F 207 LYS cc_start: 0.8951 (mttm) cc_final: 0.8714 (mmmt) REVERT: F 294 MET cc_start: 0.8999 (tmm) cc_final: 0.8661 (tmm) REVERT: F 374 MET cc_start: 0.8248 (ppp) cc_final: 0.7962 (ppp) REVERT: G 98 ASN cc_start: 0.8903 (t0) cc_final: 0.8426 (t0) REVERT: G 161 MET cc_start: 0.8930 (tmm) cc_final: 0.8130 (tmm) REVERT: G 374 MET cc_start: 0.8351 (tmm) cc_final: 0.7945 (tmm) REVERT: G 387 MET cc_start: 0.8504 (ttm) cc_final: 0.8182 (ttp) REVERT: H 36 TRP cc_start: 0.8865 (m100) cc_final: 0.7659 (m100) REVERT: H 80 MET cc_start: 0.8382 (ptm) cc_final: 0.7772 (ptm) REVERT: H 100 TYR cc_start: 0.8673 (t80) cc_final: 0.8239 (t80) REVERT: H 110 HIS cc_start: 0.7336 (m-70) cc_final: 0.6951 (m-70) REVERT: L 32 TYR cc_start: 0.8909 (m-80) cc_final: 0.7968 (m-80) REVERT: L 89 MET cc_start: 0.8494 (tpt) cc_final: 0.7691 (tpt) outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.1483 time to fit residues: 42.6363 Evaluate side-chains 132 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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: 7.9990 chunk 2 optimal weight: 8.9990 chunk 171 optimal weight: 0.0670 chunk 43 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 153 optimal weight: 0.2980 chunk 81 optimal weight: 0.0980 chunk 143 optimal weight: 0.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN B 653 GLN C 602 GLN E 202 GLN E 254 GLN E 392 ASN F 151 GLN G 254 GLN ** G 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 ASN 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 = 0.3548 r_free = 0.3548 target = 0.064756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.047944 restraints weight = 116350.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.049511 restraints weight = 63206.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.050510 restraints weight = 44101.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.051110 restraints weight = 35666.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.051455 restraints weight = 31528.218| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21545 Z= 0.142 Angle : 0.822 9.587 29813 Z= 0.364 Chirality : 0.044 0.384 4118 Planarity : 0.004 0.050 3172 Dihedral : 5.147 32.187 2307 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.02 % Favored : 92.89 % Rotamer: Outliers : 0.05 % Allowed : 3.62 % Favored : 96.32 % 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 are not related in a simple way. whole: -1.23 (0.18), residues: 2109 helix: 0.83 (0.27), residues: 387 sheet: -0.74 (0.22), residues: 557 loop : -1.44 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 579 TYR 0.015 0.001 TYR B 586 PHE 0.019 0.002 PHE H 29 TRP 0.012 0.001 TRP F 139 HIS 0.007 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (21203) covalent geometry : angle 0.75201 / 0.35 (28828) SS BOND : bond 0.00458 / 0.24 ( 41) SS BOND : angle 1.47084 / 1.18 ( 82) hydrogen bonds : bond 0.04962 / 3.34 ( 526) hydrogen bonds : angle 5.75573 / 4.22 ( 1374) link_ALPHA1-2 : bond 0.00723 / 0.49 ( 11) link_ALPHA1-2 : angle 2.59086 / 1.72 ( 33) link_ALPHA1-3 : bond 0.00632 / 0.43 ( 48) link_ALPHA1-3 : angle 1.74410 / 1.21 ( 144) link_ALPHA1-6 : bond 0.00525 / 0.37 ( 34) link_ALPHA1-6 : angle 1.44218 / 1.08 ( 102) link_BETA1-4 : bond 0.00513 / 0.35 ( 133) link_BETA1-4 : angle 1.78092 / 1.30 ( 399) link_NAG-ASN : bond 0.00425 / 0.28 ( 75) link_NAG-ASN : angle 2.59181 / 1.77 ( 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 193 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.653 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: 0.9525 (t0) cc_final: 0.9023 (t0) REVERT: B 658 TYR cc_start: 0.5899 (p90) cc_final: 0.5295 (p90) REVERT: C 530 MET cc_start: 0.7431 (mtt) cc_final: 0.6690 (mmt) REVERT: C 596 TRP cc_start: 0.8736 (m-10) cc_final: 0.8404 (m-10) REVERT: E 52 LEU cc_start: 0.9379 (mt) cc_final: 0.9155 (mt) REVERT: E 98 ASN cc_start: 0.8366 (t0) cc_final: 0.7692 (t0) REVERT: E 106 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8045 (tm-30) REVERT: E 294 MET cc_start: 0.8514 (tmm) cc_final: 0.8087 (tmm) REVERT: F 129 MET cc_start: 0.8456 (mtp) cc_final: 0.8077 (mtp) REVERT: F 207 LYS cc_start: 0.8875 (mttm) cc_final: 0.8604 (mmmt) REVERT: F 237 MET cc_start: 0.8651 (ttp) cc_final: 0.7993 (ttt) REVERT: F 292 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8687 (mt) REVERT: F 294 MET cc_start: 0.8975 (tmm) cc_final: 0.8639 (tmm) REVERT: F 374 MET cc_start: 0.8301 (ppp) cc_final: 0.7870 (ppp) REVERT: F 387 MET cc_start: 0.9139 (mmp) cc_final: 0.8914 (mmm) REVERT: G 98 ASN cc_start: 0.8664 (t0) cc_final: 0.8208 (t0) REVERT: G 161 MET cc_start: 0.8956 (tmm) cc_final: 0.7897 (tmm) REVERT: G 292 LEU cc_start: 0.8752 (mp) cc_final: 0.8338 (mt) REVERT: G 374 MET cc_start: 0.8232 (tmm) cc_final: 0.7985 (tmm) REVERT: H 35 HIS cc_start: 0.9047 (m90) cc_final: 0.8538 (m-70) REVERT: H 36 TRP cc_start: 0.8724 (m100) cc_final: 0.7368 (m100) REVERT: H 80 MET cc_start: 0.8396 (ptm) cc_final: 0.7882 (ptm) REVERT: H 100 ARG cc_start: 0.8008 (mtp-110) cc_final: 0.7486 (ppt170) REVERT: H 100 TYR cc_start: 0.8509 (t80) cc_final: 0.8297 (t80) REVERT: H 100 LEU cc_start: 0.9478 (tt) cc_final: 0.9238 (tt) REVERT: H 110 HIS cc_start: 0.7281 (m-70) cc_final: 0.6462 (p-80) REVERT: L 32 TYR cc_start: 0.8787 (m-80) cc_final: 0.7929 (m-80) REVERT: L 89 MET cc_start: 0.8773 (tpt) cc_final: 0.8069 (tpt) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.1366 time to fit residues: 41.7289 Evaluate side-chains 145 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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: 10.0000 chunk 57 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN B 629 GLN C 540 GLN C 575 ASN E 202 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN F 208 HIS G 254 GLN G 410 GLN ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.059542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.042501 restraints weight = 122949.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.043920 restraints weight = 68386.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044817 restraints weight = 48624.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045351 restraints weight = 39904.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.045678 restraints weight = 35654.209| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 21545 Z= 0.372 Angle : 1.090 11.145 29813 Z= 0.489 Chirality : 0.049 0.396 4118 Planarity : 0.006 0.062 3172 Dihedral : 6.000 39.071 2307 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.72 % Favored : 91.18 % Rotamer: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.63 % 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 are not related in a simple way. whole: -1.73 (0.18), residues: 2109 helix: 0.33 (0.25), residues: 395 sheet: -1.08 (0.24), residues: 439 loop : -1.71 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 439 TYR 0.024 0.003 TYR C 658 PHE 0.025 0.003 PHE H 100D TRP 0.037 0.003 TRP E 258 HIS 0.012 0.002 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00791 / 0.37 (21203) covalent geometry : angle 1.02203 / 0.47 (28828) SS BOND : bond 0.00521 / 0.35 ( 41) SS BOND : angle 1.92821 / 1.51 ( 82) hydrogen bonds : bond 0.05646 / 3.84 ( 526) hydrogen bonds : angle 6.16707 / 4.56 ( 1374) link_ALPHA1-2 : bond 0.00474 / 0.31 ( 11) link_ALPHA1-2 : angle 2.91791 / 2.01 ( 33) link_ALPHA1-3 : bond 0.00580 / 0.38 ( 48) link_ALPHA1-3 : angle 1.94875 / 1.39 ( 144) link_ALPHA1-6 : bond 0.00468 / 0.29 ( 34) link_ALPHA1-6 : angle 1.87922 / 1.40 ( 102) link_BETA1-4 : bond 0.00618 / 0.43 ( 133) link_BETA1-4 : angle 2.06026 / 1.48 ( 399) link_NAG-ASN : bond 0.00905 / 0.60 ( 75) link_NAG-ASN : angle 3.06260 / 2.20 ( 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 159 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8486 (tpp) cc_final: 0.8231 (tpp) REVERT: A 594 ASN cc_start: 0.9593 (t0) cc_final: 0.9152 (t0) REVERT: B 658 TYR cc_start: 0.6255 (p90) cc_final: 0.5811 (p90) REVERT: C 530 MET cc_start: 0.7667 (mtt) cc_final: 0.6955 (mmt) REVERT: C 596 TRP cc_start: 0.8971 (m-10) cc_final: 0.8646 (m-10) REVERT: E 52 LEU cc_start: 0.9393 (mt) cc_final: 0.9146 (mt) REVERT: E 294 MET cc_start: 0.8868 (tmm) cc_final: 0.8314 (tmm) REVERT: F 129 MET cc_start: 0.8645 (mtp) cc_final: 0.8379 (mtp) REVERT: F 161 MET cc_start: 0.9049 (tpp) cc_final: 0.8612 (tpp) REVERT: F 207 LYS cc_start: 0.8999 (mttm) cc_final: 0.8760 (mmmt) REVERT: F 294 MET cc_start: 0.8967 (tmm) cc_final: 0.8569 (tmm) REVERT: F 310 MET cc_start: 0.8404 (ppp) cc_final: 0.7867 (ppp) REVERT: F 374 MET cc_start: 0.8490 (ppp) cc_final: 0.8045 (ppp) REVERT: F 387 MET cc_start: 0.9374 (mmp) cc_final: 0.8847 (mmm) REVERT: G 161 MET cc_start: 0.9042 (tmm) cc_final: 0.8549 (tmm) REVERT: G 251 MET cc_start: 0.8533 (tmm) cc_final: 0.8263 (tmm) REVERT: H 80 MET cc_start: 0.8668 (ptm) cc_final: 0.8092 (ptm) REVERT: H 91 TYR cc_start: 0.8396 (m-80) cc_final: 0.8125 (m-80) REVERT: H 100 TYR cc_start: 0.8988 (t80) cc_final: 0.8128 (t80) REVERT: H 100 GLU cc_start: 0.8167 (pt0) cc_final: 0.7957 (pt0) REVERT: H 110 HIS cc_start: 0.7229 (m-70) cc_final: 0.7022 (m-70) REVERT: L 32 TYR cc_start: 0.8941 (m-80) cc_final: 0.7986 (m-80) REVERT: L 89 MET cc_start: 0.8720 (tpt) cc_final: 0.8406 (tpt) outliers start: 1 outliers final: 1 residues processed: 159 average time/residue: 0.1420 time to fit residues: 35.4776 Evaluate side-chains 121 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN C 575 ASN E 202 GLN ** E 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.044254 restraints weight = 118154.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045755 restraints weight = 63927.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.046716 restraints weight = 44667.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.047294 restraints weight = 36213.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.047644 restraints weight = 32101.650| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21545 Z= 0.176 Angle : 0.886 16.063 29813 Z= 0.391 Chirality : 0.045 0.380 4118 Planarity : 0.004 0.055 3172 Dihedral : 5.617 35.807 2307 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.40 % Favored : 92.46 % Rotamer: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % 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 are not related in a simple way. whole: -1.64 (0.18), residues: 2109 helix: 0.52 (0.25), residues: 409 sheet: -0.97 (0.25), residues: 437 loop : -1.75 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 579 TYR 0.016 0.002 TYR E 415 PHE 0.015 0.002 PHE A 600 TRP 0.022 0.002 TRP G 460 HIS 0.007 0.001 HIS G 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (21203) covalent geometry : angle 0.82355 / 0.38 (28828) SS BOND : bond 0.00555 / 0.25 ( 41) SS BOND : angle 1.43591 / 1.23 ( 82) hydrogen bonds : bond 0.04809 / 3.27 ( 526) hydrogen bonds : angle 5.77436 / 4.28 ( 1374) link_ALPHA1-2 : bond 0.00545 / 0.37 ( 11) link_ALPHA1-2 : angle 2.61202 / 1.72 ( 33) link_ALPHA1-3 : bond 0.00602 / 0.40 ( 48) link_ALPHA1-3 : angle 1.73772 / 1.21 ( 144) link_ALPHA1-6 : bond 0.00487 / 0.34 ( 34) link_ALPHA1-6 : angle 1.50746 / 1.13 ( 102) link_BETA1-4 : bond 0.00472 / 0.33 ( 133) link_BETA1-4 : angle 1.74207 / 1.26 ( 399) link_NAG-ASN : bond 0.00408 / 0.26 ( 75) link_NAG-ASN : angle 2.65374 / 1.83 ( 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 167 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.722 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 530 MET cc_start: 0.8412 (tpp) cc_final: 0.7931 (tpp) REVERT: A 594 ASN cc_start: 0.9522 (t0) cc_final: 0.9120 (t0) REVERT: A 639 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8521 (mm-30) REVERT: A 651 ILE cc_start: 0.8535 (mt) cc_final: 0.7823 (mt) REVERT: B 658 TYR cc_start: 0.6002 (p90) cc_final: 0.5608 (p90) REVERT: C 530 MET cc_start: 0.7514 (mtt) cc_final: 0.6852 (mmt) REVERT: C 580 VAL cc_start: 0.9567 (p) cc_final: 0.9242 (p) REVERT: C 596 TRP cc_start: 0.8869 (m-10) cc_final: 0.8619 (m-10) REVERT: E 52 LEU cc_start: 0.9352 (mt) cc_final: 0.9126 (mt) REVERT: E 98 ASN cc_start: 0.8600 (t0) cc_final: 0.7926 (t0) REVERT: E 471 MET cc_start: 0.8759 (mtp) cc_final: 0.8168 (ttm) REVERT: F 129 MET cc_start: 0.8650 (mtp) cc_final: 0.8321 (mtp) REVERT: F 161 MET cc_start: 0.9018 (tpp) cc_final: 0.8466 (tpp) REVERT: F 194 ASN cc_start: 0.9117 (t0) cc_final: 0.8900 (t0) REVERT: F 207 LYS cc_start: 0.8953 (mttm) cc_final: 0.8693 (mmmt) REVERT: F 294 MET cc_start: 0.8964 (tmm) cc_final: 0.8523 (tmm) REVERT: F 310 MET cc_start: 0.8584 (ppp) cc_final: 0.8137 (ppp) REVERT: F 374 MET cc_start: 0.8380 (ppp) cc_final: 0.8049 (ppp) REVERT: F 387 MET cc_start: 0.9213 (mmp) cc_final: 0.8916 (mmm) REVERT: G 67 ASP cc_start: 0.8355 (m-30) cc_final: 0.7920 (m-30) REVERT: G 98 ASN cc_start: 0.8921 (t0) cc_final: 0.8479 (t0) REVERT: G 161 MET cc_start: 0.8897 (tmm) cc_final: 0.8296 (tmm) REVERT: G 251 MET cc_start: 0.8543 (tmm) cc_final: 0.8273 (tmm) REVERT: H 57 LEU cc_start: 0.6984 (tp) cc_final: 0.6615 (pp) REVERT: H 80 MET cc_start: 0.8472 (ptm) cc_final: 0.8077 (ptm) REVERT: H 100 ASP cc_start: 0.8584 (p0) cc_final: 0.8302 (p0) REVERT: H 100 TYR cc_start: 0.8822 (t80) cc_final: 0.8332 (t80) REVERT: L 32 TYR cc_start: 0.8872 (m-80) cc_final: 0.7923 (m-80) REVERT: L 89 MET cc_start: 0.8870 (tpt) cc_final: 0.8492 (tpt) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.1422 time to fit residues: 37.1244 Evaluate side-chains 125 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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: 5.9990 chunk 203 optimal weight: 9.9990 chunk 158 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 136 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN E 202 GLN E 254 GLN E 318 GLN ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 HIS G 254 GLN G 392 ASN ** G 428 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 = 0.3464 r_free = 0.3464 target = 0.062115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.045074 restraints weight = 117755.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.046587 restraints weight = 63846.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047562 restraints weight = 44611.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048160 restraints weight = 36152.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048508 restraints weight = 31984.757| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4604 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= 0.139 Angle : 0.829 10.733 29813 Z= 0.367 Chirality : 0.044 0.378 4118 Planarity : 0.004 0.054 3172 Dihedral : 5.399 34.672 2307 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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 are not related in a simple way. whole: -1.50 (0.18), residues: 2109 helix: 0.51 (0.25), residues: 406 sheet: -0.80 (0.25), residues: 467 loop : -1.64 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 633 TYR 0.018 0.001 TYR C 586 PHE 0.017 0.002 PHE C 600 TRP 0.014 0.001 TRP F 139 HIS 0.007 0.001 HIS G 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (21203) covalent geometry : angle 0.76926 / 0.35 (28828) SS BOND : bond 0.00454 / 0.21 ( 41) SS BOND : angle 1.30052 / 1.08 ( 82) hydrogen bonds : bond 0.04378 / 2.94 ( 526) hydrogen bonds : angle 5.54481 / 4.10 ( 1374) link_ALPHA1-2 : bond 0.00573 / 0.39 ( 11) link_ALPHA1-2 : angle 2.52703 / 1.65 ( 33) link_ALPHA1-3 : bond 0.00602 / 0.41 ( 48) link_ALPHA1-3 : angle 1.65810 / 1.16 ( 144) link_ALPHA1-6 : bond 0.00504 / 0.35 ( 34) link_ALPHA1-6 : angle 1.43691 / 1.07 ( 102) link_BETA1-4 : bond 0.00465 / 0.32 ( 133) link_BETA1-4 : angle 1.64222 / 1.20 ( 399) link_NAG-ASN : bond 0.00371 / 0.23 ( 75) link_NAG-ASN : angle 2.48544 / 1.74 ( 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 167 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8333 (tpp) cc_final: 0.7881 (tpp) REVERT: A 594 ASN cc_start: 0.9543 (t0) cc_final: 0.9031 (t0) REVERT: A 639 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8545 (mm-30) REVERT: B 658 TYR cc_start: 0.5838 (p90) cc_final: 0.5513 (p90) REVERT: C 530 MET cc_start: 0.7499 (mtt) cc_final: 0.6647 (mmt) REVERT: C 596 TRP cc_start: 0.8856 (m-10) cc_final: 0.8595 (m-10) REVERT: E 52 LEU cc_start: 0.9300 (mt) cc_final: 0.9084 (mt) REVERT: E 98 ASN cc_start: 0.8266 (t0) cc_final: 0.7577 (t0) REVERT: E 471 MET cc_start: 0.8746 (mtp) cc_final: 0.8078 (ttm) REVERT: F 129 MET cc_start: 0.8434 (mtp) cc_final: 0.8045 (mtp) REVERT: F 161 MET cc_start: 0.9009 (tpp) cc_final: 0.8377 (tpp) REVERT: F 194 ASN cc_start: 0.9064 (t0) cc_final: 0.8819 (t0) REVERT: F 207 LYS cc_start: 0.8933 (mttm) cc_final: 0.8580 (mmmt) REVERT: F 294 MET cc_start: 0.8957 (tmm) cc_final: 0.8514 (tmm) REVERT: F 310 MET cc_start: 0.8583 (ppp) cc_final: 0.8105 (ppp) REVERT: F 374 MET cc_start: 0.8507 (ppp) cc_final: 0.8123 (ppp) REVERT: F 387 MET cc_start: 0.9184 (mmp) cc_final: 0.8810 (mmm) REVERT: G 67 ASP cc_start: 0.8433 (m-30) cc_final: 0.8027 (m-30) REVERT: G 98 ASN cc_start: 0.8763 (t0) cc_final: 0.8359 (t0) REVERT: G 161 MET cc_start: 0.8972 (tmm) cc_final: 0.8385 (tmm) REVERT: G 251 MET cc_start: 0.8516 (tmm) cc_final: 0.8215 (tmm) REVERT: H 48 MET cc_start: 0.6996 (mtp) cc_final: 0.6640 (mtp) REVERT: H 57 LEU cc_start: 0.7096 (tp) cc_final: 0.6683 (pp) REVERT: H 80 MET cc_start: 0.8319 (ptm) cc_final: 0.7919 (ptm) REVERT: H 91 TYR cc_start: 0.8361 (m-80) cc_final: 0.7676 (m-80) REVERT: H 100 ASP cc_start: 0.8429 (p0) cc_final: 0.8132 (p0) REVERT: H 100 TYR cc_start: 0.8776 (t80) cc_final: 0.8252 (t80) REVERT: H 100 LEU cc_start: 0.9482 (tt) cc_final: 0.9237 (tt) REVERT: L 32 TYR cc_start: 0.8894 (m-80) cc_final: 0.8092 (m-80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1306 time to fit residues: 34.9600 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 : 0.723 ------------------------------------------------------------------------------- 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: 4.9990 chunk 52 optimal weight: 0.7980 chunk 49 optimal weight: 0.0370 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN C 575 ASN 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 392 ASN ** G 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.062060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.045080 restraints weight = 119783.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.046593 restraints weight = 65876.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.047545 restraints weight = 46420.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048122 restraints weight = 37867.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.048451 restraints weight = 33677.248| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21545 Z= 0.148 Angle : 0.826 10.857 29813 Z= 0.368 Chirality : 0.044 0.376 4118 Planarity : 0.004 0.068 3172 Dihedral : 5.313 34.213 2307 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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 are not related in a simple way. whole: -1.48 (0.18), residues: 2109 helix: 0.50 (0.26), residues: 402 sheet: -0.77 (0.25), residues: 437 loop : -1.61 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 354 TYR 0.018 0.001 TYR B 658 PHE 0.019 0.002 PHE C 600 TRP 0.034 0.001 TRP F 273 HIS 0.006 0.001 HIS G 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (21203) covalent geometry : angle 0.76718 / 0.36 (28828) SS BOND : bond 0.00319 / 0.19 ( 41) SS BOND : angle 1.25705 / 1.02 ( 82) hydrogen bonds : bond 0.04364 / 2.92 ( 526) hydrogen bonds : angle 5.54341 / 4.07 ( 1374) link_ALPHA1-2 : bond 0.00517 / 0.34 ( 11) link_ALPHA1-2 : angle 2.48585 / 1.63 ( 33) link_ALPHA1-3 : bond 0.00577 / 0.39 ( 48) link_ALPHA1-3 : angle 1.65112 / 1.15 ( 144) link_ALPHA1-6 : bond 0.00480 / 0.33 ( 34) link_ALPHA1-6 : angle 1.45014 / 1.08 ( 102) link_BETA1-4 : bond 0.00460 / 0.32 ( 133) link_BETA1-4 : angle 1.61672 / 1.17 ( 399) link_NAG-ASN : bond 0.00396 / 0.25 ( 75) link_NAG-ASN : angle 2.48035 / 1.77 ( 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 163 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8327 (tpp) cc_final: 0.7878 (tpp) REVERT: A 594 ASN cc_start: 0.9539 (t0) cc_final: 0.9159 (t0) REVERT: A 639 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8534 (mm-30) REVERT: B 588 LYS cc_start: 0.9473 (tmtt) cc_final: 0.9102 (mtpp) REVERT: B 589 ASP cc_start: 0.9232 (m-30) cc_final: 0.8895 (m-30) REVERT: B 658 TYR cc_start: 0.5789 (p90) cc_final: 0.5447 (p90) REVERT: C 530 MET cc_start: 0.7475 (mtt) cc_final: 0.6627 (mmt) REVERT: C 596 TRP cc_start: 0.8851 (m-10) cc_final: 0.8427 (m-10) REVERT: E 98 ASN cc_start: 0.8300 (t0) cc_final: 0.7580 (t0) REVERT: E 471 MET cc_start: 0.8702 (mtp) cc_final: 0.8087 (ttm) REVERT: F 161 MET cc_start: 0.8968 (tpp) cc_final: 0.8314 (tpp) REVERT: F 194 ASN cc_start: 0.9046 (t0) cc_final: 0.8790 (t0) REVERT: F 207 LYS cc_start: 0.8987 (mttm) cc_final: 0.8542 (mmmt) REVERT: F 237 MET cc_start: 0.8811 (ttm) cc_final: 0.8480 (ttm) REVERT: F 294 MET cc_start: 0.8957 (tmm) cc_final: 0.8537 (tmm) REVERT: F 374 MET cc_start: 0.8485 (ppp) cc_final: 0.8119 (ppp) REVERT: F 387 MET cc_start: 0.9192 (mmp) cc_final: 0.8802 (mmm) REVERT: G 67 ASP cc_start: 0.8423 (m-30) cc_final: 0.8047 (m-30) REVERT: G 98 ASN cc_start: 0.8780 (t0) cc_final: 0.8280 (t0) REVERT: G 161 MET cc_start: 0.9018 (tmm) cc_final: 0.8471 (tmm) REVERT: G 251 MET cc_start: 0.8595 (tmm) cc_final: 0.8268 (tmm) REVERT: H 57 LEU cc_start: 0.7101 (tp) cc_final: 0.6860 (tp) REVERT: H 80 MET cc_start: 0.8323 (ptm) cc_final: 0.7908 (ptm) REVERT: H 91 TYR cc_start: 0.8416 (m-80) cc_final: 0.7783 (m-80) REVERT: H 100 ASP cc_start: 0.8352 (p0) cc_final: 0.8041 (p0) REVERT: H 100 TYR cc_start: 0.8773 (t80) cc_final: 0.8257 (t80) REVERT: H 100 LEU cc_start: 0.9448 (tt) cc_final: 0.9188 (tt) REVERT: L 32 TYR cc_start: 0.8930 (m-80) cc_final: 0.8128 (m-80) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1327 time to fit residues: 35.0719 Evaluate side-chains 123 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 0.7980 chunk 26 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 60 optimal weight: 0.0010 chunk 170 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 199 optimal weight: 40.0000 chunk 87 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN B 629 GLN E 202 GLN ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS G 254 GLN G 392 ASN ** G 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.062963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.045882 restraints weight = 117422.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.047443 restraints weight = 63248.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048440 restraints weight = 43962.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049043 restraints weight = 35467.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049414 restraints weight = 31372.741| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4844 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= 0.132 Angle : 0.811 10.386 29813 Z= 0.364 Chirality : 0.044 0.385 4118 Planarity : 0.004 0.056 3172 Dihedral : 5.259 33.837 2307 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.21 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.18), residues: 2109 helix: 0.43 (0.26), residues: 402 sheet: -0.92 (0.23), residues: 500 loop : -1.51 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 633 TYR 0.016 0.001 TYR B 658 PHE 0.019 0.001 PHE C 600 TRP 0.034 0.001 TRP F 273 HIS 0.006 0.001 HIS G 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (21203) covalent geometry : angle 0.75708 / 0.35 (28828) SS BOND : bond 0.00343 / 0.19 ( 41) SS BOND : angle 1.39001 / 1.16 ( 82) hydrogen bonds : bond 0.04222 / 2.81 ( 526) hydrogen bonds : angle 5.53703 / 4.04 ( 1374) link_ALPHA1-2 : bond 0.00591 / 0.40 ( 11) link_ALPHA1-2 : angle 2.42814 / 1.58 ( 33) link_ALPHA1-3 : bond 0.00592 / 0.40 ( 48) link_ALPHA1-3 : angle 1.61573 / 1.12 ( 144) link_ALPHA1-6 : bond 0.00513 / 0.35 ( 34) link_ALPHA1-6 : angle 1.40087 / 1.04 ( 102) link_BETA1-4 : bond 0.00471 / 0.32 ( 133) link_BETA1-4 : angle 1.57004 / 1.14 ( 399) link_NAG-ASN : bond 0.00356 / 0.22 ( 75) link_NAG-ASN : angle 2.30505 / 1.63 ( 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 166 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8153 (tpp) cc_final: 0.7743 (tpp) REVERT: A 594 ASN cc_start: 0.9576 (t0) cc_final: 0.9098 (t0) REVERT: A 639 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8514 (mm-30) REVERT: B 574 LYS cc_start: 0.8366 (mttt) cc_final: 0.7351 (mttt) REVERT: B 588 LYS cc_start: 0.9461 (tmtt) cc_final: 0.9106 (mtpp) REVERT: B 589 ASP cc_start: 0.9241 (m-30) cc_final: 0.8920 (m-30) REVERT: B 658 TYR cc_start: 0.5656 (p90) cc_final: 0.5404 (p90) REVERT: C 530 MET cc_start: 0.7441 (mtt) cc_final: 0.6592 (mmt) REVERT: C 596 TRP cc_start: 0.8901 (m-10) cc_final: 0.8554 (m-10) REVERT: E 52 LEU cc_start: 0.9337 (mt) cc_final: 0.9074 (mt) REVERT: E 98 ASN cc_start: 0.8190 (t0) cc_final: 0.7534 (t0) REVERT: E 471 MET cc_start: 0.8656 (mtp) cc_final: 0.8025 (ttm) REVERT: F 69 TRP cc_start: 0.7396 (p90) cc_final: 0.6920 (p90) REVERT: F 129 MET cc_start: 0.8323 (mtp) cc_final: 0.8033 (mtp) REVERT: F 194 ASN cc_start: 0.9046 (t0) cc_final: 0.8809 (t0) REVERT: F 207 LYS cc_start: 0.8940 (mttm) cc_final: 0.8529 (mmmt) REVERT: F 237 MET cc_start: 0.8735 (ttm) cc_final: 0.8435 (ttm) REVERT: F 292 LEU cc_start: 0.9262 (mp) cc_final: 0.9058 (mt) REVERT: F 294 MET cc_start: 0.8947 (tmm) cc_final: 0.8512 (tmm) REVERT: F 310 MET cc_start: 0.8490 (ppp) cc_final: 0.7916 (ppp) REVERT: F 374 MET cc_start: 0.8473 (ppp) cc_final: 0.8134 (ppp) REVERT: F 387 MET cc_start: 0.9112 (mmp) cc_final: 0.8678 (mmm) REVERT: G 67 ASP cc_start: 0.8440 (m-30) cc_final: 0.8124 (m-30) REVERT: G 98 ASN cc_start: 0.8579 (t0) cc_final: 0.8156 (t0) REVERT: G 161 MET cc_start: 0.8986 (tmm) cc_final: 0.8502 (tmm) REVERT: G 251 MET cc_start: 0.8664 (tmm) cc_final: 0.8352 (tmm) REVERT: H 48 MET cc_start: 0.6908 (mtp) cc_final: 0.6677 (mtp) REVERT: H 57 LEU cc_start: 0.7088 (tp) cc_final: 0.6843 (tp) REVERT: H 80 MET cc_start: 0.8123 (ptm) cc_final: 0.7737 (ptm) REVERT: H 91 TYR cc_start: 0.8453 (m-80) cc_final: 0.7818 (m-80) REVERT: H 100 ASP cc_start: 0.8343 (p0) cc_final: 0.7241 (p0) REVERT: H 100 TYR cc_start: 0.8718 (t80) cc_final: 0.8492 (t80) REVERT: H 100 LEU cc_start: 0.9409 (tt) cc_final: 0.9139 (tt) REVERT: L 32 TYR cc_start: 0.8928 (m-80) cc_final: 0.8160 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1258 time to fit residues: 33.9316 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 : 0.693 ------------------------------------------------------------------------------- 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: 0.9990 chunk 163 optimal weight: 0.0980 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 202 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 206 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 overall best weight: 1.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN E 202 GLN E 318 GLN ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 392 ASN ** G 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.062579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.045772 restraints weight = 117674.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.047289 restraints weight = 65004.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.048243 restraints weight = 45708.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.048831 restraints weight = 37160.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.049161 restraints weight = 32916.855| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4962 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= 0.132 Angle : 0.800 11.004 29813 Z= 0.359 Chirality : 0.043 0.379 4118 Planarity : 0.004 0.058 3172 Dihedral : 5.193 34.522 2307 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.35 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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 are not related in a simple way. whole: -1.43 (0.18), residues: 2109 helix: 0.44 (0.26), residues: 402 sheet: -0.81 (0.23), residues: 488 loop : -1.53 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 354 TYR 0.018 0.001 TYR B 658 PHE 0.021 0.002 PHE C 600 TRP 0.029 0.001 TRP F 273 HIS 0.006 0.001 HIS G 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (21203) covalent geometry : angle 0.74684 / 0.35 (28828) SS BOND : bond 0.00308 / 0.17 ( 41) SS BOND : angle 1.32192 / 1.12 ( 82) hydrogen bonds : bond 0.04234 / 2.86 ( 526) hydrogen bonds : angle 5.50849 / 4.03 ( 1374) link_ALPHA1-2 : bond 0.00533 / 0.35 ( 11) link_ALPHA1-2 : angle 2.38720 / 1.56 ( 33) link_ALPHA1-3 : bond 0.00563 / 0.38 ( 48) link_ALPHA1-3 : angle 1.60387 / 1.12 ( 144) link_ALPHA1-6 : bond 0.00489 / 0.34 ( 34) link_ALPHA1-6 : angle 1.41538 / 1.05 ( 102) link_BETA1-4 : bond 0.00461 / 0.31 ( 133) link_BETA1-4 : angle 1.55086 / 1.12 ( 399) link_NAG-ASN : bond 0.00333 / 0.20 ( 75) link_NAG-ASN : angle 2.23451 / 1.58 ( 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 161 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8142 (tpp) cc_final: 0.7730 (tpp) REVERT: A 594 ASN cc_start: 0.9580 (t0) cc_final: 0.9109 (t0) REVERT: A 630 GLU cc_start: 0.9408 (pt0) cc_final: 0.9197 (pt0) REVERT: A 639 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8419 (mm-30) REVERT: B 530 MET cc_start: 0.8463 (tpp) cc_final: 0.8251 (mmm) REVERT: B 574 LYS cc_start: 0.8527 (mttt) cc_final: 0.7884 (mttt) REVERT: B 588 LYS cc_start: 0.9455 (tmtt) cc_final: 0.9090 (mtpp) REVERT: B 589 ASP cc_start: 0.9222 (m-30) cc_final: 0.8904 (m-30) REVERT: B 658 TYR cc_start: 0.5503 (p90) cc_final: 0.5232 (p90) REVERT: C 530 MET cc_start: 0.7439 (mtt) cc_final: 0.6593 (mmt) REVERT: C 596 TRP cc_start: 0.8866 (m-10) cc_final: 0.8493 (m-10) REVERT: E 52 LEU cc_start: 0.9320 (mt) cc_final: 0.9069 (mt) REVERT: E 98 ASN cc_start: 0.8145 (t0) cc_final: 0.7549 (t0) REVERT: E 471 MET cc_start: 0.8651 (mtp) cc_final: 0.8084 (ttm) REVERT: F 69 TRP cc_start: 0.7371 (p90) cc_final: 0.7015 (p90) REVERT: F 129 MET cc_start: 0.8339 (mtp) cc_final: 0.8057 (mtp) REVERT: F 194 ASN cc_start: 0.9034 (t0) cc_final: 0.8779 (t0) REVERT: F 207 LYS cc_start: 0.8888 (mttm) cc_final: 0.8502 (mmmt) REVERT: F 237 MET cc_start: 0.8750 (ttm) cc_final: 0.8514 (ttm) REVERT: F 294 MET cc_start: 0.8986 (tmm) cc_final: 0.8572 (tmm) REVERT: F 310 MET cc_start: 0.8623 (ppp) cc_final: 0.8114 (ppp) REVERT: F 374 MET cc_start: 0.8476 (ppp) cc_final: 0.8102 (ppp) REVERT: G 67 ASP cc_start: 0.8442 (m-30) cc_final: 0.8128 (m-30) REVERT: G 98 ASN cc_start: 0.8494 (t0) cc_final: 0.8092 (t0) REVERT: G 161 MET cc_start: 0.8967 (tmm) cc_final: 0.8491 (tmm) REVERT: G 251 MET cc_start: 0.8585 (tmm) cc_final: 0.8257 (tmm) REVERT: H 48 MET cc_start: 0.6939 (mtp) cc_final: 0.6624 (mtp) REVERT: H 57 LEU cc_start: 0.7125 (tp) cc_final: 0.6745 (tp) REVERT: H 80 MET cc_start: 0.8142 (ptm) cc_final: 0.7819 (ptm) REVERT: H 91 TYR cc_start: 0.8423 (m-80) cc_final: 0.7797 (m-80) REVERT: H 100 TYR cc_start: 0.8568 (t80) cc_final: 0.8133 (t80) REVERT: H 100 LEU cc_start: 0.9392 (tt) cc_final: 0.9136 (tt) REVERT: L 32 TYR cc_start: 0.8936 (m-80) cc_final: 0.8191 (m-80) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1337 time to fit residues: 34.7767 Evaluate side-chains 125 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 143 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 179 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 chunk 204 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN E 202 GLN ** E 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN G 392 ASN ** G 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.062829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.046016 restraints weight = 116629.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047516 restraints weight = 64623.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.048476 restraints weight = 45626.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049068 restraints weight = 37139.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049417 restraints weight = 32917.606| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21545 Z= 0.128 Angle : 0.791 12.274 29813 Z= 0.355 Chirality : 0.043 0.383 4118 Planarity : 0.004 0.059 3172 Dihedral : 5.118 35.191 2307 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.54 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.33 (0.18), residues: 2109 helix: 0.56 (0.26), residues: 386 sheet: -0.88 (0.23), residues: 482 loop : -1.38 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 354 TYR 0.018 0.001 TYR B 658 PHE 0.020 0.002 PHE C 600 TRP 0.026 0.001 TRP F 273 HIS 0.005 0.001 HIS G 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (21203) covalent geometry : angle 0.74089 / 0.34 (28828) SS BOND : bond 0.00297 / 0.17 ( 41) SS BOND : angle 1.20776 / 1.01 ( 82) hydrogen bonds : bond 0.04154 / 2.78 ( 526) hydrogen bonds : angle 5.45598 / 3.98 ( 1374) link_ALPHA1-2 : bond 0.00550 / 0.37 ( 11) link_ALPHA1-2 : angle 2.34175 / 1.53 ( 33) link_ALPHA1-3 : bond 0.00563 / 0.38 ( 48) link_ALPHA1-3 : angle 1.59231 / 1.11 ( 144) link_ALPHA1-6 : bond 0.00495 / 0.34 ( 34) link_ALPHA1-6 : angle 1.40183 / 1.04 ( 102) link_BETA1-4 : bond 0.00468 / 0.32 ( 133) link_BETA1-4 : angle 1.53067 / 1.11 ( 399) link_NAG-ASN : bond 0.00341 / 0.21 ( 75) link_NAG-ASN : angle 2.16064 / 1.53 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.23 seconds wall clock time: 49 minutes 50.36 seconds (2990.36 seconds total)