Starting phenix.real_space_refine on Sat Mar 7 01:29:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n1v_9319/03_2026/6n1v_9319_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n1v_9319/03_2026/6n1v_9319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n1v_9319/03_2026/6n1v_9319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n1v_9319/03_2026/6n1v_9319.map" model { file = "/net/cci-nas-00/data/ceres_data/6n1v_9319/03_2026/6n1v_9319_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n1v_9319/03_2026/6n1v_9319_neut.cif" } resolution = 4.0 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= 0.012 sd= 0.109 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 177 5.16 5 C 22872 2.51 5 N 6054 2.21 5 O 7395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36498 Number of models: 1 Model: "" Number of chains: 69 Chain: "3" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1669 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Chain: "4" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1612 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain: "B" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "Y" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "a" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "g" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "i" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "1" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1669 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Chain: "2" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1612 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain: "A" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "E" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "X" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "Z" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "f" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "h" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "C" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1669 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 209} Chain: "L" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1612 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 787 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "Q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "0" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "BA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "CA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "DA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.14, per 1000 atoms: 0.25 Number of scatterers: 36498 At special positions: 0 Unit cell: (190.4, 185.92, 157.92, 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 177 16.00 O 7395 8.00 N 6054 7.00 C 22872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 97 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 149 " - pdb=" SG CYS 3 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 225 " - pdb=" SG CYS 4 215 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 22 " - pdb=" SG CYS 4 89 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 138 " - pdb=" SG CYS 4 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 92 " distance=2.03 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 88 " distance=2.03 Simple disulfide: pdb=" SG CYS g 22 " - pdb=" SG CYS g 103 " distance=2.04 Simple disulfide: pdb=" SG CYS g 109 " - pdb=" SG CYS g 112 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 22 " - pdb=" SG CYS 1 97 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 149 " - pdb=" SG CYS 1 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 225 " - pdb=" SG CYS 2 215 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 22 " - pdb=" SG CYS 2 89 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 138 " - pdb=" SG CYS 2 197 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.01 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 23 " - pdb=" SG CYS Z 88 " distance=2.03 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 103 " distance=2.04 Simple disulfide: pdb=" SG CYS f 109 " - pdb=" SG CYS f 112 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS H 225 " - pdb=" SG CYS L 215 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 103 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 112 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA W 3 " - " MAN W 4 " " BMA b 3 " - " MAN b 4 " " BMA j 3 " - " MAN j 4 " " BMA l 3 " - " MAN l 4 " " BMA s 3 " - " MAN s 4 " " BMA t 3 " - " MAN t 4 " " BMA x 3 " - " MAN x 4 " " BMA z 3 " - " MAN z 4 " " BMAAA 3 " - " MANAA 4 " " BMABA 3 " - " MANBA 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA W 3 " - " MAN W 5 " " BMA l 3 " - " MAN l 5 " " BMA s 3 " - " MAN s 5 " " BMA z 3 " - " MAN z 5 " " BMAAA 3 " - " MANAA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " 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 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 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 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 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 q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 0 1 " - " ASN C 133 " " NAG 5 1 " - " ASN C 137 " " NAG 6 1 " - " ASN C 156 " " NAG 7 1 " - " ASN C 301 " " NAG 8 1 " - " ASN C 332 " " NAG 9 1 " - " ASN C 448 " " NAG A 608 " - " ASN A 339 " " NAG A 617 " - " ASN A 392 " " NAG A 623 " - " ASN A 197 " " NAG B 608 " - " ASN B 339 " " NAG B 617 " - " ASN B 392 " " NAG B 623 " - " ASN B 197 " " NAG C 608 " - " ASN C 339 " " NAG C 617 " - " ASN C 392 " " NAG C 623 " - " ASN C 197 " " NAG G 1 " - " ASN B 160 " " NAG I 1 " - " ASN B 295 " " NAG J 1 " - " ASN B 363 " " NAG K 1 " - " ASN B 386 " " NAG O 1 " - " ASN B 133 " " NAG P 1 " - " ASN B 137 " " NAG S 1 " - " ASN B 156 " " NAG T 1 " - " ASN B 301 " " NAG U 1 " - " ASN B 332 " " NAG V 1 " - " ASN B 448 " " NAG W 1 " - " ASN B 262 " " NAG b 1 " - " ASN B 276 " " NAG c 1 " - " ASN B 234 " " NAG d 1 " - " ASN B 88 " " NAG e 1 " - " ASN A 160 " " NAG j 1 " - " ASN A 295 " " NAG k 1 " - " ASN A 363 " " NAG l 1 " - " ASN A 386 " " NAG m 1 " - " ASN A 133 " " NAG n 1 " - " ASN A 137 " " NAG o 1 " - " ASN A 156 " " NAG p 1 " - " ASN A 301 " " NAG q 1 " - " ASN A 332 " " NAG r 1 " - " ASN A 448 " " NAG s 1 " - " ASN A 262 " " NAG t 1 " - " ASN A 276 " " NAG u 1 " - " ASN A 234 " " NAG v 1 " - " ASN A 88 " " NAG w 1 " - " ASN C 160 " " NAG x 1 " - " ASN C 295 " " NAG y 1 " - " ASN C 363 " " NAG z 1 " - " ASN C 386 " " NAGAA 1 " - " ASN C 262 " " NAGBA 1 " - " ASN C 276 " " NAGCA 1 " - " ASN C 234 " " NAGDA 1 " - " ASN C 88 " Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 87 sheets defined 14.1% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain '3' and resid 63 through 66 Processing helix chain '3' and resid 88 through 92 removed outlier: 3.752A pdb=" N THR 3 92 " --> pdb=" O ALA 3 89 " (cutoff:3.500A) Processing helix chain '3' and resid 140 through 142 No H-bonds generated for 'chain '3' and resid 140 through 142' Processing helix chain '3' and resid 196 through 199 removed outlier: 4.006A pdb=" N GLY 3 199 " --> pdb=" O SER 3 196 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 196 through 199' Processing helix chain '4' and resid 80 through 84 removed outlier: 3.761A pdb=" N GLU 4 84 " --> pdb=" O SER 4 81 " (cutoff:3.500A) Processing helix chain '4' and resid 125 through 131 Processing helix chain '4' and resid 186 through 190 Processing helix chain '4' and resid 211 through 215 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 100 through 115 removed outlier: 3.726A pdb=" N ILE B 109 " --> pdb=" O HIS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.733A pdb=" N LEU B 125 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.647A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 475 through 481 removed outlier: 4.147A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 528 removed outlier: 4.456A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 543 removed outlier: 3.575A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 removed outlier: 3.745A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 616 removed outlier: 4.440A pdb=" N SER F 615 " --> pdb=" O ASN F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 removed outlier: 3.851A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 618 through 623' Processing helix chain 'F' and resid 627 through 635 removed outlier: 4.034A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 641 through 664 Processing helix chain 'Y' and resid 83 through 87 removed outlier: 3.711A pdb=" N SER Y 87 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 83 Processing helix chain 'g' and resid 28 through 32 removed outlier: 3.563A pdb=" N ASP g 31 " --> pdb=" O ASN g 28 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR g 32 " --> pdb=" O PHE g 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 28 through 32' Processing helix chain 'g' and resid 94 through 98 removed outlier: 3.708A pdb=" N THR g 98 " --> pdb=" O PRO g 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 83 Processing helix chain '1' and resid 63 through 66 Processing helix chain '1' and resid 88 through 92 removed outlier: 3.752A pdb=" N THR 1 92 " --> pdb=" O ALA 1 89 " (cutoff:3.500A) Processing helix chain '1' and resid 140 through 142 No H-bonds generated for 'chain '1' and resid 140 through 142' Processing helix chain '1' and resid 196 through 199 removed outlier: 4.007A pdb=" N GLY 1 199 " --> pdb=" O SER 1 196 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 196 through 199' Processing helix chain '2' and resid 80 through 84 removed outlier: 3.761A pdb=" N GLU 2 84 " --> pdb=" O SER 2 81 " (cutoff:3.500A) Processing helix chain '2' and resid 125 through 131 Processing helix chain '2' and resid 186 through 190 Processing helix chain '2' and resid 211 through 215 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 100 through 115 removed outlier: 3.726A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.733A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.647A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.147A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 528 removed outlier: 4.456A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 537 through 543 removed outlier: 3.575A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 595 removed outlier: 3.744A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 616 removed outlier: 4.441A pdb=" N SER E 615 " --> pdb=" O ASN E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 623 removed outlier: 3.850A pdb=" N ILE E 622 " --> pdb=" O ASN E 618 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TRP E 623 " --> pdb=" O LEU E 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 618 through 623' Processing helix chain 'E' and resid 627 through 635 removed outlier: 4.034A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 641 through 664 Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.711A pdb=" N SER X 87 " --> pdb=" O ALA X 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 83 Processing helix chain 'f' and resid 28 through 32 removed outlier: 3.562A pdb=" N ASP f 31 " --> pdb=" O ASN f 28 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR f 32 " --> pdb=" O PHE f 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 28 through 32' Processing helix chain 'f' and resid 94 through 98 removed outlier: 3.708A pdb=" N THR f 98 " --> pdb=" O PRO f 95 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 83 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 100 through 115 removed outlier: 3.726A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.733A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.647A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 475 through 481 removed outlier: 4.146A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 528 removed outlier: 4.456A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.575A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 removed outlier: 3.745A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.440A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 removed outlier: 3.850A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 618 through 623' Processing helix chain 'D' and resid 627 through 635 removed outlier: 4.033A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 Processing helix chain 'H' and resid 63 through 66 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.752A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 142 No H-bonds generated for 'chain 'H' and resid 140 through 142' Processing helix chain 'H' and resid 196 through 199 removed outlier: 4.007A pdb=" N GLY H 199 " --> pdb=" O SER H 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 196 through 199' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.762A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 186 through 190 Processing helix chain 'L' and resid 211 through 215 Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.711A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.563A pdb=" N ASP Q 31 " --> pdb=" O ASN Q 28 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.708A pdb=" N THR Q 98 " --> pdb=" O PRO Q 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain '3' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain '3' and resid 11 through 12 removed outlier: 3.773A pdb=" N GLY 3 50 " --> pdb=" O TRP 3 37 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG 3 39 " --> pdb=" O TRP 3 48 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP 3 48 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR 3 185 " --> pdb=" O ASP 3 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR 3 185 " --> pdb=" O ASP 3 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 159 through 163 removed outlier: 4.364A pdb=" N TYR 3 203 " --> pdb=" O VAL 3 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '4' and resid 9 through 12 removed outlier: 6.570A pdb=" N MET 4 10 " --> pdb=" O THR 4 108 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP 4 36 " --> pdb=" O LEU 4 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '4' and resid 9 through 12 removed outlier: 6.570A pdb=" N MET 4 10 " --> pdb=" O THR 4 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '4' and resid 18 through 23 Processing sheet with id=AA9, first strand: chain '4' and resid 118 through 122 removed outlier: 5.821A pdb=" N TYR 4 176 " --> pdb=" O ASP 4 142 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER 4 179 " --> pdb=" O LYS 4 167 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS 4 167 " --> pdb=" O SER 4 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR 4 181 " --> pdb=" O THR 4 165 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR 4 165 " --> pdb=" O TYR 4 181 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER 4 183 " --> pdb=" O VAL 4 163 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL 4 163 " --> pdb=" O SER 4 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '4' and resid 148 through 153 Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 39 Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 76 removed outlier: 4.079A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.697A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.551A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 271 through 273 removed outlier: 7.682A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 271 through 273 removed outlier: 11.364A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 312 removed outlier: 3.777A pdb=" N LYS B 305 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'Y' and resid 11 through 12 removed outlier: 4.320A pdb=" N TYR Y 33 " --> pdb=" O THR Y 95 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP Y 34 " --> pdb=" O TYR Y 50 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR Y 50 " --> pdb=" O TRP Y 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP Y 36 " --> pdb=" O ILE Y 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AC5, first strand: chain 'a' and resid 19 through 20 Processing sheet with id=AC6, first strand: chain 'a' and resid 44 through 48 removed outlier: 6.736A pdb=" N TRP a 35 " --> pdb=" O ILE a 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 3 through 5 Processing sheet with id=AC8, first strand: chain 'g' and resid 10 through 12 removed outlier: 6.332A pdb=" N ARG g 38 " --> pdb=" O TRP g 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP g 47 " --> pdb=" O ARG g 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE g 40 " --> pdb=" O PHE g 45 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE g 45 " --> pdb=" O ILE g 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'g' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'i' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'i' and resid 10 through 13 removed outlier: 6.382A pdb=" N TRP i 35 " --> pdb=" O LEU i 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '1' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain '1' and resid 11 through 12 removed outlier: 3.774A pdb=" N GLY 1 50 " --> pdb=" O TRP 1 37 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG 1 39 " --> pdb=" O TRP 1 48 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP 1 48 " --> pdb=" O ARG 1 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '1' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR 1 185 " --> pdb=" O ASP 1 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '1' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR 1 185 " --> pdb=" O ASP 1 153 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '1' and resid 159 through 163 removed outlier: 4.364A pdb=" N TYR 1 203 " --> pdb=" O VAL 1 220 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '2' and resid 9 through 12 removed outlier: 6.569A pdb=" N MET 2 10 " --> pdb=" O THR 2 108 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP 2 36 " --> pdb=" O LEU 2 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '2' and resid 9 through 12 removed outlier: 6.569A pdb=" N MET 2 10 " --> pdb=" O THR 2 108 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '2' and resid 18 through 23 Processing sheet with id=AE2, first strand: chain '2' and resid 118 through 122 removed outlier: 5.822A pdb=" N TYR 2 176 " --> pdb=" O ASP 2 142 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N SER 2 179 " --> pdb=" O LYS 2 167 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS 2 167 " --> pdb=" O SER 2 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR 2 181 " --> pdb=" O THR 2 165 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR 2 165 " --> pdb=" O TYR 2 181 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER 2 183 " --> pdb=" O VAL 2 163 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL 2 163 " --> pdb=" O SER 2 183 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '2' and resid 148 through 153 Processing sheet with id=AE4, first strand: chain 'A' and resid 35 through 39 Processing sheet with id=AE5, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AE6, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.079A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.697A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AE9, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.551A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.682A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.363A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.772A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 304 through 312 removed outlier: 3.778A pdb=" N LYS A 305 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AF5, first strand: chain 'X' and resid 11 through 12 removed outlier: 4.320A pdb=" N TYR X 33 " --> pdb=" O THR X 95 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP X 34 " --> pdb=" O TYR X 50 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR X 50 " --> pdb=" O TRP X 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP X 36 " --> pdb=" O ILE X 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 11 through 12 Processing sheet with id=AF7, first strand: chain 'Z' and resid 19 through 20 Processing sheet with id=AF8, first strand: chain 'Z' and resid 44 through 48 removed outlier: 6.736A pdb=" N TRP Z 35 " --> pdb=" O ILE Z 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'f' and resid 3 through 5 Processing sheet with id=AG1, first strand: chain 'f' and resid 10 through 12 removed outlier: 6.332A pdb=" N ARG f 38 " --> pdb=" O TRP f 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP f 47 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE f 40 " --> pdb=" O PHE f 45 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE f 45 " --> pdb=" O ILE f 40 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'f' and resid 10 through 12 Processing sheet with id=AG3, first strand: chain 'h' and resid 4 through 7 Processing sheet with id=AG4, first strand: chain 'h' and resid 10 through 13 removed outlier: 6.382A pdb=" N TRP h 35 " --> pdb=" O LEU h 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AG6, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AG7, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.080A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.697A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AH1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.551A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.682A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.364A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.950A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.788A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 304 through 312 removed outlier: 3.777A pdb=" N LYS C 305 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.773A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 129 through 133 removed outlier: 6.020A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 159 through 163 removed outlier: 4.364A pdb=" N TYR H 203 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.570A pdb=" N MET L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.570A pdb=" N MET L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AI4, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.820A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER L 179 " --> pdb=" O LYS L 167 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS L 167 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N TYR L 181 " --> pdb=" O THR L 165 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR L 165 " --> pdb=" O TYR L 181 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER L 183 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL L 163 " --> pdb=" O SER L 183 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 148 through 153 Processing sheet with id=AI6, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AI7, first strand: chain 'M' and resid 11 through 12 removed outlier: 4.320A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AI9, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AJ1, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.736A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AJ3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.333A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Q' and resid 10 through 12 Processing sheet with id=AJ5, first strand: chain 'R' and resid 4 through 7 Processing sheet with id=AJ6, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.382A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 1347 hydrogen bonds defined for protein. 3384 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: 9.38 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11253 1.34 - 1.46: 8475 1.46 - 1.57: 17346 1.57 - 1.69: 3 1.69 - 1.81: 228 Bond restraints: 37305 Sorted by residual: bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.334 1.373 -0.040 8.40e-03 1.42e+04 2.22e+01 bond pdb=" C THR B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 1.334 1.372 -0.039 8.40e-03 1.42e+04 2.14e+01 bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.334 1.372 -0.038 8.40e-03 1.42e+04 2.10e+01 bond pdb=" N PHE i 91 " pdb=" CA PHE i 91 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.29e+01 bond pdb=" N PHE h 91 " pdb=" CA PHE h 91 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.27e+01 ... (remaining 37300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 49555 2.86 - 5.72: 1022 5.72 - 8.59: 150 8.59 - 11.45: 18 11.45 - 14.31: 9 Bond angle restraints: 50754 Sorted by residual: angle pdb=" C GLN h 90 " pdb=" N PHE h 91 " pdb=" CA PHE h 91 " ideal model delta sigma weight residual 121.54 134.53 -12.99 1.91e+00 2.74e-01 4.62e+01 angle pdb=" C GLN i 90 " pdb=" N PHE i 91 " pdb=" CA PHE i 91 " ideal model delta sigma weight residual 121.54 134.51 -12.97 1.91e+00 2.74e-01 4.61e+01 angle pdb=" C GLN R 90 " pdb=" N PHE R 91 " pdb=" CA PHE R 91 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" N GLN h 90 " pdb=" CA GLN h 90 " pdb=" C GLN h 90 " ideal model delta sigma weight residual 110.36 101.36 9.00 1.55e+00 4.16e-01 3.37e+01 angle pdb=" N GLN i 90 " pdb=" CA GLN i 90 " pdb=" C GLN i 90 " ideal model delta sigma weight residual 110.36 101.38 8.98 1.55e+00 4.16e-01 3.36e+01 ... (remaining 50749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.40: 21651 22.40 - 44.79: 1563 44.79 - 67.19: 450 67.19 - 89.58: 213 89.58 - 111.98: 126 Dihedral angle restraints: 24003 sinusoidal: 11184 harmonic: 12819 Sorted by residual: dihedral pdb=" CA SER R 7 " pdb=" C SER R 7 " pdb=" N PRO R 8 " pdb=" CA PRO R 8 " ideal model delta harmonic sigma weight residual -180.00 -98.58 -81.42 0 5.00e+00 4.00e-02 2.65e+02 dihedral pdb=" CA SER i 7 " pdb=" C SER i 7 " pdb=" N PRO i 8 " pdb=" CA PRO i 8 " ideal model delta harmonic sigma weight residual 180.00 -98.59 -81.41 0 5.00e+00 4.00e-02 2.65e+02 dihedral pdb=" CA SER h 7 " pdb=" C SER h 7 " pdb=" N PRO h 8 " pdb=" CA PRO h 8 " ideal model delta harmonic sigma weight residual -180.00 -98.63 -81.37 0 5.00e+00 4.00e-02 2.65e+02 ... (remaining 24000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 5875 0.133 - 0.267: 173 0.267 - 0.400: 39 0.400 - 0.533: 6 0.533 - 0.666: 3 Chirality restraints: 6096 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN B 156 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG 6 1 " pdb=" ND2 ASN C 156 " pdb=" C2 NAG 6 1 " pdb=" O5 NAG 6 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C1 NAG o 1 " pdb=" ND2 ASN A 156 " pdb=" C2 NAG o 1 " pdb=" O5 NAG o 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 6093 not shown) Planarity restraints: 6327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE i 91 " 0.034 2.00e-02 2.50e+03 6.50e-02 4.23e+01 pdb=" C PHE i 91 " -0.113 2.00e-02 2.50e+03 pdb=" O PHE i 91 " 0.041 2.00e-02 2.50e+03 pdb=" N GLU i 96 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 91 " -0.034 2.00e-02 2.50e+03 6.50e-02 4.23e+01 pdb=" C PHE R 91 " 0.113 2.00e-02 2.50e+03 pdb=" O PHE R 91 " -0.041 2.00e-02 2.50e+03 pdb=" N GLU R 96 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE h 91 " -0.034 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C PHE h 91 " 0.112 2.00e-02 2.50e+03 pdb=" O PHE h 91 " -0.041 2.00e-02 2.50e+03 pdb=" N GLU h 96 " -0.037 2.00e-02 2.50e+03 ... (remaining 6324 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 6844 2.76 - 3.30: 31701 3.30 - 3.83: 60920 3.83 - 4.37: 64905 4.37 - 4.90: 113565 Nonbonded interactions: 277935 Sorted by model distance: nonbonded pdb=" O THR A 387 " pdb=" OG1 THR A 387 " model vdw 2.226 3.040 nonbonded pdb=" O THR B 387 " pdb=" OG1 THR B 387 " model vdw 2.226 3.040 nonbonded pdb=" O THR C 387 " pdb=" OG1 THR C 387 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN F 611 " pdb=" OG SER F 613 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASN D 611 " pdb=" OG SER D 613 " model vdw 2.260 3.040 ... (remaining 277930 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: 0.08 Found NCS groups: ncs_group { reference = chain '0' selection = chain '7' selection = chain '9' selection = chain 'O' selection = chain 'T' selection = chain 'V' selection = chain 'm' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'H' } ncs_group { reference = chain '2' selection = chain '4' selection = chain 'L' } ncs_group { reference = chain '5' selection = chain '6' selection = chain '8' selection = chain 'CA' selection = chain 'DA' selection = chain 'G' selection = chain 'J' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'AA' selection = chain 'K' selection = chain 'W' selection = chain 'l' selection = chain 's' selection = chain 'z' } ncs_group { reference = chain 'BA' selection = chain 'I' selection = chain 'b' selection = chain 'j' selection = chain 't' selection = chain 'x' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'Q' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'R' selection = chain 'h' selection = chain 'i' } 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: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 37.670 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.008 0.067 37503 Z= 0.394 Angle : 1.115 19.967 51294 Z= 0.551 Chirality : 0.065 0.666 6096 Planarity : 0.008 0.089 6276 Dihedral : 20.265 111.976 15633 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.68 % Favored : 93.12 % Rotamer: Outliers : 10.74 % Allowed : 13.07 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.07 % 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: -2.97 (0.11), residues: 4404 helix: -2.46 (0.18), residues: 435 sheet: -1.23 (0.12), residues: 1611 loop : -2.44 (0.11), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 105 TYR 0.021 0.002 TYR X 100B PHE 0.035 0.003 PHE A 288 TRP 0.016 0.002 TRP X 36 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00827 (37305) covalent geometry : angle 1.04641 (50754) SS BOND : bond 0.00509 ( 54) SS BOND : angle 1.14756 ( 108) hydrogen bonds : bond 0.12580 ( 1242) hydrogen bonds : angle 7.45116 ( 3384) link_ALPHA1-3 : bond 0.00764 ( 12) link_ALPHA1-3 : angle 3.25098 ( 36) link_ALPHA1-6 : bond 0.00190 ( 6) link_ALPHA1-6 : angle 2.05185 ( 18) link_BETA1-4 : bond 0.00896 ( 75) link_BETA1-4 : angle 3.93708 ( 225) link_NAG-ASN : bond 0.00755 ( 51) link_NAG-ASN : angle 5.16323 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 414 poor density : 306 time to evaluate : 1.332 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: symmetry clash REVERT: B 265 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8441 (pp) REVERT: B 374 HIS cc_start: 0.9343 (OUTLIER) cc_final: 0.7951 (p90) REVERT: B 377 ASN cc_start: 0.8742 (t0) cc_final: 0.8341 (p0) REVERT: B 480 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8169 (mtt90) REVERT: Y 57 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8026 (t) REVERT: g 70 MET cc_start: 0.8352 (mtt) cc_final: 0.8008 (mtt) REVERT: g 122 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8545 (pt0) REVERT: 2 184 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.4740 (mp) REVERT: A 265 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8325 (pp) REVERT: A 480 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8652 (mtt90) REVERT: X 57 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8043 (t) REVERT: Z 93 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8178 (t) REVERT: f 122 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8649 (pt0) REVERT: C 34 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7688 (mm) REVERT: C 265 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8254 (pp) REVERT: C 480 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8716 (mtt90) REVERT: H 208 ASN cc_start: 0.4587 (OUTLIER) cc_final: 0.4076 (t0) REVERT: M 57 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8185 (t) REVERT: M 95 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.6567 (t) REVERT: N 93 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8606 (t) outliers start: 414 outliers final: 128 residues processed: 689 average time/residue: 0.2409 time to fit residues: 264.1155 Evaluate side-chains 295 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 149 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 28 ASN Chi-restraints excluded: chain 4 residue 95 SER Chi-restraints excluded: chain 4 residue 148 VAL Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 183 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 44 GLN Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain a residue 93 SER Chi-restraints excluded: chain g residue 33 SER Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain i residue 82 ASP Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 172 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 191 VAL Chi-restraints excluded: chain 1 residue 210 LYS Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 28 ASN Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 2 residue 179 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 26 GLU Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain Z residue 93 SER Chi-restraints excluded: chain f residue 33 SER Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 90 GLN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 208 ASN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 179 SER Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 82 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 0.0170 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0870 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 2.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 111 HIS 3 180 GLN 4 99 HIS 4 112 GLN ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN B 287 GLN B 377 ASN F 575 GLN F 607 ASN ** a 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 GLN g 65 GLN 1 111 HIS ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 180 GLN 2 99 HIS 2 112 GLN ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 ASN A 103 GLN A 246 GLN A 287 GLN A 377 ASN A 432 GLN A 478 ASN E 575 GLN E 607 ASN ** Z 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 6 GLN f 65 GLN C 80 ASN C 103 GLN C 246 GLN C 287 GLN C 377 ASN D 575 GLN D 607 ASN H 111 HIS H 180 GLN ** H 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 HIS L 112 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN Q 6 GLN Q 65 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.058282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.041228 restraints weight = 279548.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.041904 restraints weight = 162853.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.041926 restraints weight = 114998.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.042213 restraints weight = 82499.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.042179 restraints weight = 77524.756| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37503 Z= 0.135 Angle : 0.810 13.588 51294 Z= 0.376 Chirality : 0.050 0.442 6096 Planarity : 0.006 0.068 6276 Dihedral : 14.858 88.310 7960 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.47 % Favored : 94.37 % Rotamer: Outliers : 4.90 % Allowed : 17.41 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.12), residues: 4404 helix: -0.75 (0.24), residues: 438 sheet: -0.75 (0.12), residues: 1641 loop : -1.85 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 588 TYR 0.016 0.001 TYR M 100O PHE 0.023 0.001 PHE F 522 TRP 0.019 0.001 TRP 4 189 HIS 0.008 0.001 HIS 1 209 Details of bonding type rmsd covalent geometry : bond 0.00291 (37305) covalent geometry : angle 0.76046 (50754) SS BOND : bond 0.00247 ( 54) SS BOND : angle 0.74318 ( 108) hydrogen bonds : bond 0.03807 ( 1242) hydrogen bonds : angle 6.15084 ( 3384) link_ALPHA1-3 : bond 0.01223 ( 12) link_ALPHA1-3 : angle 2.30788 ( 36) link_ALPHA1-6 : bond 0.00855 ( 6) link_ALPHA1-6 : angle 2.24143 ( 18) link_BETA1-4 : bond 0.00504 ( 75) link_BETA1-4 : angle 2.93467 ( 225) link_NAG-ASN : bond 0.00514 ( 51) link_NAG-ASN : angle 3.61191 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 211 time to evaluate : 1.158 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: 3 154 TYR cc_start: 0.8890 (p90) cc_final: 0.8101 (p90) REVERT: 4 86 ASP cc_start: 0.7397 (m-30) cc_final: 0.6761 (t0) REVERT: 4 179 SER cc_start: 0.0803 (OUTLIER) cc_final: 0.0320 (m) REVERT: B 44 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8554 (m) REVERT: B 95 MET cc_start: 0.9090 (ptm) cc_final: 0.7736 (ppp) REVERT: B 265 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8624 (pp) REVERT: F 632 ASP cc_start: 0.9355 (t0) cc_final: 0.9125 (p0) REVERT: Y 100 MET cc_start: 0.9149 (mmm) cc_final: 0.8468 (mmm) REVERT: g 70 MET cc_start: 0.9185 (mtt) cc_final: 0.8842 (mtt) REVERT: 1 154 TYR cc_start: 0.8677 (p90) cc_final: 0.8111 (p90) REVERT: 2 86 ASP cc_start: 0.7509 (m-30) cc_final: 0.6837 (t0) REVERT: 2 179 SER cc_start: 0.2004 (OUTLIER) cc_final: 0.1729 (m) REVERT: A 95 MET cc_start: 0.9294 (ptm) cc_final: 0.8205 (ppp) REVERT: A 265 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8544 (pp) REVERT: A 416 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8220 (pt) REVERT: E 629 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9007 (tt) REVERT: E 632 ASP cc_start: 0.9384 (t0) cc_final: 0.9117 (p0) REVERT: C 44 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8651 (m) REVERT: C 95 MET cc_start: 0.9327 (ptm) cc_final: 0.8737 (ppp) REVERT: C 104 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8148 (tpt) REVERT: C 161 MET cc_start: 0.8629 (tpt) cc_final: 0.8026 (tpt) REVERT: C 265 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8510 (pp) REVERT: C 370 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: C 416 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8491 (pt) REVERT: D 601 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8455 (ttpt) REVERT: H 154 TYR cc_start: 0.8783 (p90) cc_final: 0.8176 (p90) REVERT: L 100 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8596 (p) REVERT: M 95 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.7837 (t) REVERT: M 100 MET cc_start: 0.9128 (mmm) cc_final: 0.8558 (mmm) outliers start: 189 outliers final: 110 residues processed: 393 average time/residue: 0.2230 time to fit residues: 143.5098 Evaluate side-chains 272 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 147 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 141 SER Chi-restraints excluded: chain 4 residue 148 VAL Chi-restraints excluded: chain 4 residue 179 SER Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 185 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 210 LYS Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 141 SER Chi-restraints excluded: chain 2 residue 148 VAL Chi-restraints excluded: chain 2 residue 179 SER Chi-restraints excluded: chain 2 residue 185 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain f residue 11 ILE Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 141 SER Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 418 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 252 optimal weight: 0.0010 chunk 141 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 180 GLN ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 GLN B 432 GLN a 38 GLN g 65 GLN 1 180 GLN ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN Z 38 GLN f 65 GLN f 122 GLN C 432 GLN H 180 GLN ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Q 65 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.057969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.040444 restraints weight = 280201.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.041685 restraints weight = 160145.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.041428 restraints weight = 100075.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.041378 restraints weight = 77030.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.041411 restraints weight = 79105.779| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37503 Z= 0.129 Angle : 0.728 13.030 51294 Z= 0.336 Chirality : 0.049 0.426 6096 Planarity : 0.005 0.069 6276 Dihedral : 11.853 87.929 7854 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.90 % Favored : 93.89 % Rotamer: Outliers : 4.46 % Allowed : 18.13 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.12), residues: 4404 helix: -0.01 (0.26), residues: 420 sheet: -0.46 (0.12), residues: 1665 loop : -1.66 (0.12), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 588 TYR 0.010 0.001 TYR B 384 PHE 0.017 0.001 PHE D 522 TRP 0.009 0.001 TRP F 631 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00276 (37305) covalent geometry : angle 0.67577 (50754) SS BOND : bond 0.00384 ( 54) SS BOND : angle 0.65633 ( 108) hydrogen bonds : bond 0.03573 ( 1242) hydrogen bonds : angle 5.72628 ( 3384) link_ALPHA1-3 : bond 0.01069 ( 12) link_ALPHA1-3 : angle 2.21025 ( 36) link_ALPHA1-6 : bond 0.00888 ( 6) link_ALPHA1-6 : angle 2.64046 ( 18) link_BETA1-4 : bond 0.00501 ( 75) link_BETA1-4 : angle 2.67782 ( 225) link_NAG-ASN : bond 0.00520 ( 51) link_NAG-ASN : angle 3.66614 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 169 time to evaluate : 1.613 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: 3 154 TYR cc_start: 0.8765 (p90) cc_final: 0.8520 (p90) REVERT: 4 86 ASP cc_start: 0.7432 (m-30) cc_final: 0.6714 (t0) REVERT: B 44 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8501 (m) REVERT: B 65 LYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6450 (tppt) REVERT: B 95 MET cc_start: 0.9154 (ptm) cc_final: 0.7867 (ppp) REVERT: B 265 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8608 (pp) REVERT: B 480 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.9030 (mtt90) REVERT: F 601 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8326 (ttpp) REVERT: F 632 ASP cc_start: 0.9380 (t0) cc_final: 0.9116 (p0) REVERT: Y 100 MET cc_start: 0.9193 (mmm) cc_final: 0.8530 (mmm) REVERT: g 70 MET cc_start: 0.9193 (mtt) cc_final: 0.8839 (mtt) REVERT: 1 154 TYR cc_start: 0.8523 (p90) cc_final: 0.8058 (p90) REVERT: 2 86 ASP cc_start: 0.7543 (m-30) cc_final: 0.6794 (t0) REVERT: 2 100 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8494 (p) REVERT: A 95 MET cc_start: 0.9337 (ptm) cc_final: 0.8300 (ppp) REVERT: A 252 LYS cc_start: 0.9586 (OUTLIER) cc_final: 0.9382 (mtpp) REVERT: A 265 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8586 (pp) REVERT: A 416 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8175 (pt) REVERT: E 629 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9178 (tt) REVERT: E 632 ASP cc_start: 0.9422 (t0) cc_final: 0.9116 (p0) REVERT: X 44 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: X 100 MET cc_start: 0.9135 (mmm) cc_final: 0.8509 (mmm) REVERT: f 65 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8462 (tt0) REVERT: C 44 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8701 (m) REVERT: C 95 MET cc_start: 0.9339 (ptm) cc_final: 0.8380 (ppp) REVERT: C 104 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8418 (tpt) REVERT: C 161 MET cc_start: 0.8646 (tpt) cc_final: 0.8045 (tpt) REVERT: C 252 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9277 (ptpp) REVERT: C 265 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8470 (pp) REVERT: C 370 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: C 480 ARG cc_start: 0.9376 (OUTLIER) cc_final: 0.8972 (tpp80) REVERT: D 601 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: H 154 TYR cc_start: 0.8572 (p90) cc_final: 0.8016 (p90) REVERT: M 44 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8463 (pm20) REVERT: M 95 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.7882 (t) REVERT: M 100 MET cc_start: 0.9063 (mmm) cc_final: 0.8657 (mmm) outliers start: 172 outliers final: 108 residues processed: 331 average time/residue: 0.2278 time to fit residues: 125.3579 Evaluate side-chains 265 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 136 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain g residue 65 GLN Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 7 SER Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 70 SER Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 252 LYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain E residue 664 ASP Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain f residue 122 GLN Chi-restraints excluded: chain h residue 7 SER Chi-restraints excluded: chain h residue 51 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 431 optimal weight: 5.9990 chunk 399 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 386 optimal weight: 30.0000 chunk 202 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 430 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 GLN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 122 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.054272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.036357 restraints weight = 261231.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037653 restraints weight = 151780.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.037789 restraints weight = 83615.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.037701 restraints weight = 64107.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.037829 restraints weight = 69160.757| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 37503 Z= 0.198 Angle : 0.751 13.215 51294 Z= 0.348 Chirality : 0.048 0.429 6096 Planarity : 0.005 0.070 6276 Dihedral : 10.688 85.870 7827 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.90 % Favored : 92.89 % Rotamer: Outliers : 5.14 % Allowed : 18.00 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 4404 helix: 0.27 (0.26), residues: 420 sheet: -0.37 (0.13), residues: 1659 loop : -1.64 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG h 40 TYR 0.011 0.001 TYR 1 203 PHE 0.017 0.001 PHE B 288 TRP 0.010 0.001 TRP g 55 HIS 0.006 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00434 (37305) covalent geometry : angle 0.70140 (50754) SS BOND : bond 0.00341 ( 54) SS BOND : angle 0.75149 ( 108) hydrogen bonds : bond 0.03805 ( 1242) hydrogen bonds : angle 5.70464 ( 3384) link_ALPHA1-3 : bond 0.00997 ( 12) link_ALPHA1-3 : angle 2.26570 ( 36) link_ALPHA1-6 : bond 0.00834 ( 6) link_ALPHA1-6 : angle 2.95835 ( 18) link_BETA1-4 : bond 0.00389 ( 75) link_BETA1-4 : angle 2.54144 ( 225) link_NAG-ASN : bond 0.00463 ( 51) link_NAG-ASN : angle 3.68241 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 151 time to evaluate : 1.297 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: 3 154 TYR cc_start: 0.8822 (p90) cc_final: 0.8392 (p90) REVERT: 4 86 ASP cc_start: 0.7527 (m-30) cc_final: 0.6797 (t0) REVERT: B 65 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6505 (tppt) REVERT: B 95 MET cc_start: 0.9158 (ptm) cc_final: 0.8695 (ppp) REVERT: B 265 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8561 (pp) REVERT: B 480 ARG cc_start: 0.9455 (OUTLIER) cc_final: 0.9161 (mtt90) REVERT: F 530 MET cc_start: 0.9405 (mmm) cc_final: 0.9090 (tpp) REVERT: F 601 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8374 (ttpp) REVERT: F 632 ASP cc_start: 0.9362 (t0) cc_final: 0.9112 (p0) REVERT: Y 100 MET cc_start: 0.9166 (mmm) cc_final: 0.8456 (mmm) REVERT: g 70 MET cc_start: 0.9162 (mtt) cc_final: 0.8794 (mtt) REVERT: g 72 ARG cc_start: 0.9357 (OUTLIER) cc_final: 0.7766 (pmt-80) REVERT: g 80 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7356 (p0) REVERT: 1 29 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6548 (tp) REVERT: 1 154 TYR cc_start: 0.8683 (p90) cc_final: 0.8062 (p90) REVERT: 2 86 ASP cc_start: 0.7616 (m-30) cc_final: 0.6876 (t0) REVERT: 2 100 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8596 (p) REVERT: A 95 MET cc_start: 0.9336 (ptm) cc_final: 0.8293 (ppp) REVERT: A 265 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8557 (pp) REVERT: E 530 MET cc_start: 0.9456 (mmm) cc_final: 0.9188 (tpp) REVERT: E 629 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9210 (tt) REVERT: E 632 ASP cc_start: 0.9421 (t0) cc_final: 0.9152 (p0) REVERT: X 44 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8464 (pm20) REVERT: f 72 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.8736 (pmt-80) REVERT: f 88 MET cc_start: 0.8293 (tmm) cc_final: 0.8012 (tmm) REVERT: C 104 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8290 (tpt) REVERT: C 161 MET cc_start: 0.8622 (tpt) cc_final: 0.8104 (tpt) REVERT: C 252 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9327 (ptpp) REVERT: C 265 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8441 (pp) REVERT: C 370 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8423 (pm20) REVERT: C 480 ARG cc_start: 0.9471 (OUTLIER) cc_final: 0.9252 (mtt90) REVERT: D 601 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8492 (ttpp) REVERT: H 154 TYR cc_start: 0.8849 (p90) cc_final: 0.7929 (p90) REVERT: L 100 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8623 (p) REVERT: M 100 MET cc_start: 0.9068 (mmm) cc_final: 0.8756 (mmm) REVERT: Q 72 ARG cc_start: 0.9354 (OUTLIER) cc_final: 0.7613 (pmt-80) outliers start: 198 outliers final: 135 residues processed: 339 average time/residue: 0.2178 time to fit residues: 124.3895 Evaluate side-chains 289 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 134 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 3 residue 203 TYR Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 185 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 65 GLN Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain 1 residue 29 ILE Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain 2 residue 185 THR Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 639 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 148 optimal weight: 30.0000 chunk 284 optimal weight: 9.9990 chunk 301 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 395 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN g 65 GLN g 122 GLN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN f 35 HIS f 65 GLN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 HIS Q 122 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.052794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.035409 restraints weight = 267909.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.036408 restraints weight = 154586.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.036294 restraints weight = 97153.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.036424 restraints weight = 76010.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.036481 restraints weight = 74738.250| |-----------------------------------------------------------------------------| r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 37503 Z= 0.331 Angle : 0.879 14.389 51294 Z= 0.410 Chirality : 0.050 0.451 6096 Planarity : 0.006 0.092 6276 Dihedral : 10.647 87.282 7819 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.95 % Favored : 91.85 % Rotamer: Outliers : 5.86 % Allowed : 18.39 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.12), residues: 4404 helix: 0.07 (0.25), residues: 417 sheet: -0.44 (0.13), residues: 1575 loop : -1.81 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 54 TYR 0.014 0.002 TYR 1 96 PHE 0.024 0.002 PHE B 383 TRP 0.012 0.002 TRP f 55 HIS 0.008 0.002 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00728 (37305) covalent geometry : angle 0.83469 (50754) SS BOND : bond 0.00422 ( 54) SS BOND : angle 1.14217 ( 108) hydrogen bonds : bond 0.04625 ( 1242) hydrogen bonds : angle 6.06427 ( 3384) link_ALPHA1-3 : bond 0.00924 ( 12) link_ALPHA1-3 : angle 2.41432 ( 36) link_ALPHA1-6 : bond 0.00921 ( 6) link_ALPHA1-6 : angle 2.93377 ( 18) link_BETA1-4 : bond 0.00436 ( 75) link_BETA1-4 : angle 2.53497 ( 225) link_NAG-ASN : bond 0.00647 ( 51) link_NAG-ASN : angle 3.89474 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 122 time to evaluate : 1.403 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: 3 154 TYR cc_start: 0.8886 (p90) cc_final: 0.8303 (p90) REVERT: 4 215 CYS cc_start: 0.5547 (OUTLIER) cc_final: 0.5214 (m) REVERT: B 265 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8572 (pp) REVERT: B 480 ARG cc_start: 0.9557 (OUTLIER) cc_final: 0.9323 (mtt90) REVERT: F 601 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8399 (ttpp) REVERT: Y 100 MET cc_start: 0.9182 (mmm) cc_final: 0.8908 (mmm) REVERT: g 70 MET cc_start: 0.9160 (mtt) cc_final: 0.8807 (mtt) REVERT: g 72 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.7987 (pmt-80) REVERT: i 24 LYS cc_start: 0.9402 (tttt) cc_final: 0.9082 (tptm) REVERT: i 27 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8898 (tp40) REVERT: 1 29 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6457 (tp) REVERT: 1 154 TYR cc_start: 0.8740 (p90) cc_final: 0.8033 (p90) REVERT: 2 100 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 265 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8574 (pp) REVERT: A 480 ARG cc_start: 0.9540 (OUTLIER) cc_final: 0.8972 (mtm110) REVERT: E 530 MET cc_start: 0.9351 (mmm) cc_final: 0.9141 (tpp) REVERT: X 44 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8584 (pm20) REVERT: X 100 MET cc_start: 0.9066 (mmm) cc_final: 0.8387 (mmm) REVERT: f 72 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8451 (pmt-80) REVERT: h 17 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8591 (pt0) REVERT: h 24 LYS cc_start: 0.9437 (tttt) cc_final: 0.9007 (tptm) REVERT: h 27 GLN cc_start: 0.9341 (OUTLIER) cc_final: 0.8973 (tp40) REVERT: C 95 MET cc_start: 0.9381 (ptm) cc_final: 0.9064 (ppp) REVERT: C 265 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8412 (pp) REVERT: C 480 ARG cc_start: 0.9563 (OUTLIER) cc_final: 0.9283 (mtt90) REVERT: D 601 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8435 (ttpt) REVERT: H 154 TYR cc_start: 0.8787 (p90) cc_final: 0.7818 (p90) REVERT: L 100 VAL cc_start: 0.8924 (OUTLIER) cc_final: 0.8640 (p) REVERT: Q 65 GLN cc_start: 0.9442 (OUTLIER) cc_final: 0.9041 (tp40) REVERT: Q 72 ARG cc_start: 0.9382 (OUTLIER) cc_final: 0.8211 (pmt-80) REVERT: R 27 GLN cc_start: 0.9304 (OUTLIER) cc_final: 0.9034 (tp40) outliers start: 226 outliers final: 159 residues processed: 336 average time/residue: 0.2087 time to fit residues: 118.8127 Evaluate side-chains 296 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 116 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 185 THR Chi-restraints excluded: chain 4 residue 215 CYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 48 ILE Chi-restraints excluded: chain g residue 65 GLN Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 27 GLN Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain 1 residue 29 ILE Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain 2 residue 185 THR Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain h residue 17 GLU Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain h residue 90 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 142 ASP Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 8 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 215 optimal weight: 0.0770 chunk 357 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 373 optimal weight: 30.0000 chunk 220 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 192 HIS f 65 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.056277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.038745 restraints weight = 280185.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.039361 restraints weight = 158797.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.039591 restraints weight = 110754.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.039781 restraints weight = 82938.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.039755 restraints weight = 71216.175| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37503 Z= 0.150 Angle : 0.725 14.950 51294 Z= 0.336 Chirality : 0.047 0.409 6096 Planarity : 0.005 0.088 6276 Dihedral : 9.773 87.301 7813 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.90 % Favored : 92.89 % Rotamer: Outliers : 4.95 % Allowed : 19.46 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.12), residues: 4404 helix: 0.50 (0.26), residues: 417 sheet: -0.41 (0.13), residues: 1629 loop : -1.57 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.014 0.001 TYR M 100O PHE 0.014 0.001 PHE C 288 TRP 0.012 0.001 TRP X 36 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00330 (37305) covalent geometry : angle 0.67860 (50754) SS BOND : bond 0.00393 ( 54) SS BOND : angle 1.03248 ( 108) hydrogen bonds : bond 0.03643 ( 1242) hydrogen bonds : angle 5.65367 ( 3384) link_ALPHA1-3 : bond 0.01001 ( 12) link_ALPHA1-3 : angle 2.05744 ( 36) link_ALPHA1-6 : bond 0.00958 ( 6) link_ALPHA1-6 : angle 2.14529 ( 18) link_BETA1-4 : bond 0.00415 ( 75) link_BETA1-4 : angle 2.36108 ( 225) link_NAG-ASN : bond 0.00500 ( 51) link_NAG-ASN : angle 3.59702 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 151 time to evaluate : 1.266 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: 3 154 TYR cc_start: 0.8791 (p90) cc_final: 0.8326 (p90) REVERT: 4 86 ASP cc_start: 0.7548 (m-30) cc_final: 0.6845 (t0) REVERT: 4 215 CYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5895 (m) REVERT: B 44 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8736 (m) REVERT: B 95 MET cc_start: 0.9216 (ptm) cc_final: 0.8161 (ppp) REVERT: B 103 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8346 (pp30) REVERT: B 265 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8514 (pp) REVERT: B 480 ARG cc_start: 0.9435 (OUTLIER) cc_final: 0.9044 (mtt90) REVERT: Y 100 MET cc_start: 0.9125 (mmm) cc_final: 0.8809 (mmm) REVERT: g 70 MET cc_start: 0.9172 (mtt) cc_final: 0.8788 (mtt) REVERT: g 72 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.7829 (pmt-80) REVERT: g 80 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7264 (p0) REVERT: i 27 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8859 (tp40) REVERT: 1 29 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6475 (tp) REVERT: 1 154 TYR cc_start: 0.8737 (p90) cc_final: 0.8219 (p90) REVERT: 2 100 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8613 (p) REVERT: 2 184 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7565 (pt) REVERT: A 95 MET cc_start: 0.9388 (ptm) cc_final: 0.8468 (ppp) REVERT: A 103 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8356 (pp30) REVERT: A 265 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8525 (pp) REVERT: A 480 ARG cc_start: 0.9435 (OUTLIER) cc_final: 0.8812 (mtm110) REVERT: E 530 MET cc_start: 0.9283 (mmm) cc_final: 0.9079 (tpp) REVERT: E 632 ASP cc_start: 0.9429 (t0) cc_final: 0.9144 (p0) REVERT: X 44 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8547 (pm20) REVERT: X 100 MET cc_start: 0.9006 (mmm) cc_final: 0.8503 (mmm) REVERT: f 65 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8678 (tt0) REVERT: f 72 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8787 (pmt-80) REVERT: h 27 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8925 (tp40) REVERT: C 44 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8795 (m) REVERT: C 95 MET cc_start: 0.9323 (ptm) cc_final: 0.8457 (ppp) REVERT: C 103 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: C 265 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8434 (pp) REVERT: C 480 ARG cc_start: 0.9462 (OUTLIER) cc_final: 0.9189 (mtt90) REVERT: D 601 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8479 (ttpp) REVERT: H 154 TYR cc_start: 0.8714 (p90) cc_final: 0.8183 (p90) REVERT: L 100 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8664 (p) REVERT: M 100 MET cc_start: 0.9042 (mmm) cc_final: 0.8029 (mmm) REVERT: Q 72 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.7680 (pmt-80) REVERT: Q 88 MET cc_start: 0.8392 (tmm) cc_final: 0.7873 (tmm) REVERT: R 27 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.9007 (tp40) outliers start: 191 outliers final: 142 residues processed: 331 average time/residue: 0.2208 time to fit residues: 122.5707 Evaluate side-chains 300 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 132 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 3 residue 203 TYR Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 185 THR Chi-restraints excluded: chain 4 residue 215 CYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 27 GLN Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 1 residue 29 ILE Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 95 SER Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 184 LEU Chi-restraints excluded: chain 2 residue 185 THR Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 45 SER Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 70 MET Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 163 optimal weight: 10.0000 chunk 291 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 389 optimal weight: 20.0000 chunk 320 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 387 optimal weight: 0.2980 chunk 185 optimal weight: 10.0000 chunk 148 optimal weight: 40.0000 chunk 260 optimal weight: 10.0000 chunk 328 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN F 577 GLN g 65 GLN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN A 130 GLN E 577 GLN f 65 GLN C 130 GLN D 577 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.054613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.036573 restraints weight = 261504.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.037362 restraints weight = 144079.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.037670 restraints weight = 100151.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.037872 restraints weight = 72403.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.037980 restraints weight = 66731.814| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 37503 Z= 0.109 Angle : 0.693 15.393 51294 Z= 0.321 Chirality : 0.047 0.397 6096 Planarity : 0.005 0.088 6276 Dihedral : 9.083 86.627 7809 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 4.36 % Allowed : 20.44 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.13), residues: 4404 helix: 0.72 (0.27), residues: 417 sheet: -0.25 (0.13), residues: 1635 loop : -1.39 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 40 TYR 0.010 0.001 TYR C 435 PHE 0.017 0.001 PHE A 53 TRP 0.016 0.001 TRP Y 100J HIS 0.002 0.001 HIS 3 209 Details of bonding type rmsd covalent geometry : bond 0.00238 (37305) covalent geometry : angle 0.64737 (50754) SS BOND : bond 0.00354 ( 54) SS BOND : angle 1.13346 ( 108) hydrogen bonds : bond 0.03277 ( 1242) hydrogen bonds : angle 5.37665 ( 3384) link_ALPHA1-3 : bond 0.01016 ( 12) link_ALPHA1-3 : angle 1.98135 ( 36) link_ALPHA1-6 : bond 0.01139 ( 6) link_ALPHA1-6 : angle 2.08496 ( 18) link_BETA1-4 : bond 0.00458 ( 75) link_BETA1-4 : angle 2.27021 ( 225) link_NAG-ASN : bond 0.00555 ( 51) link_NAG-ASN : angle 3.46391 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 154 time to evaluate : 1.380 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: 3 154 TYR cc_start: 0.8751 (p90) cc_final: 0.8295 (p90) REVERT: 4 86 ASP cc_start: 0.7441 (m-30) cc_final: 0.6758 (t0) REVERT: 4 184 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7502 (pt) REVERT: 4 215 CYS cc_start: 0.6267 (OUTLIER) cc_final: 0.5903 (m) REVERT: B 44 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8670 (m) REVERT: B 95 MET cc_start: 0.9229 (ptm) cc_final: 0.8197 (ppp) REVERT: B 103 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8205 (pp30) REVERT: B 265 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8517 (pp) REVERT: B 480 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8990 (mtt90) REVERT: F 530 MET cc_start: 0.9303 (tpp) cc_final: 0.8940 (mmp) REVERT: F 632 ASP cc_start: 0.9310 (t0) cc_final: 0.9079 (p0) REVERT: F 656 ASN cc_start: 0.8903 (m-40) cc_final: 0.8653 (t0) REVERT: g 70 MET cc_start: 0.9173 (mtt) cc_final: 0.8790 (mtt) REVERT: g 72 ARG cc_start: 0.9355 (OUTLIER) cc_final: 0.7834 (pmt-80) REVERT: g 80 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7237 (p0) REVERT: i 27 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8768 (tp40) REVERT: 1 29 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6575 (tp) REVERT: 1 154 TYR cc_start: 0.8724 (p90) cc_final: 0.8207 (p90) REVERT: 2 100 VAL cc_start: 0.8927 (OUTLIER) cc_final: 0.8592 (p) REVERT: A 95 MET cc_start: 0.9355 (ptm) cc_final: 0.8436 (ppp) REVERT: A 166 ARG cc_start: 0.7901 (mmp80) cc_final: 0.7621 (mmp80) REVERT: A 265 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8518 (pp) REVERT: A 480 ARG cc_start: 0.9398 (OUTLIER) cc_final: 0.8786 (mtm110) REVERT: E 656 ASN cc_start: 0.8879 (m-40) cc_final: 0.8610 (t0) REVERT: X 44 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8518 (pm20) REVERT: X 100 MET cc_start: 0.9041 (mmm) cc_final: 0.8505 (mmm) REVERT: f 72 ARG cc_start: 0.9365 (OUTLIER) cc_final: 0.8806 (pmt-80) REVERT: f 88 MET cc_start: 0.8704 (tmm) cc_final: 0.8062 (tmm) REVERT: h 27 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8906 (tp40) REVERT: C 44 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8745 (m) REVERT: C 95 MET cc_start: 0.9215 (ptm) cc_final: 0.8366 (ppp) REVERT: C 103 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: C 265 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8417 (pp) REVERT: C 480 ARG cc_start: 0.9409 (OUTLIER) cc_final: 0.9080 (mtt90) REVERT: D 542 ARG cc_start: 0.9025 (ttm110) cc_final: 0.8780 (ttp-110) REVERT: D 601 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8552 (ttpt) REVERT: D 656 ASN cc_start: 0.8954 (m-40) cc_final: 0.8697 (t0) REVERT: H 154 TYR cc_start: 0.8657 (p90) cc_final: 0.8122 (p90) REVERT: L 100 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8660 (p) REVERT: M 44 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: M 100 MET cc_start: 0.9070 (mmm) cc_final: 0.8077 (mmm) REVERT: Q 72 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.7661 (pmt-80) REVERT: Q 88 MET cc_start: 0.8527 (tmm) cc_final: 0.8032 (tmm) REVERT: R 27 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.9000 (tp40) outliers start: 168 outliers final: 113 residues processed: 317 average time/residue: 0.2347 time to fit residues: 122.2285 Evaluate side-chains 271 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 133 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 203 TYR Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 185 THR Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain 4 residue 215 CYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 65 GLN Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 27 GLN Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 1 residue 29 ILE Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 185 THR Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 314 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 409 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 398 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 19 optimal weight: 50.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN ** g 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN D 577 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.053234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036166 restraints weight = 265554.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.037280 restraints weight = 145170.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.036918 restraints weight = 90366.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.036975 restraints weight = 75802.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.037013 restraints weight = 71262.352| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37503 Z= 0.247 Angle : 0.782 14.976 51294 Z= 0.363 Chirality : 0.048 0.427 6096 Planarity : 0.005 0.092 6276 Dihedral : 9.199 86.830 7799 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 4.80 % Allowed : 20.29 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 4404 helix: 0.56 (0.27), residues: 417 sheet: -0.27 (0.13), residues: 1599 loop : -1.57 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG h 40 TYR 0.012 0.001 TYR C 435 PHE 0.018 0.002 PHE A 288 TRP 0.017 0.002 TRP Y 100J HIS 0.006 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00550 (37305) covalent geometry : angle 0.73803 (50754) SS BOND : bond 0.00389 ( 54) SS BOND : angle 1.23995 ( 108) hydrogen bonds : bond 0.03948 ( 1242) hydrogen bonds : angle 5.61461 ( 3384) link_ALPHA1-3 : bond 0.00815 ( 12) link_ALPHA1-3 : angle 2.06876 ( 36) link_ALPHA1-6 : bond 0.00870 ( 6) link_ALPHA1-6 : angle 2.12154 ( 18) link_BETA1-4 : bond 0.00396 ( 75) link_BETA1-4 : angle 2.34833 ( 225) link_NAG-ASN : bond 0.00526 ( 51) link_NAG-ASN : angle 3.69893 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 128 time to evaluate : 1.431 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: 3 154 TYR cc_start: 0.8810 (p90) cc_final: 0.8134 (p90) REVERT: B 95 MET cc_start: 0.9202 (ptm) cc_final: 0.8981 (ppp) REVERT: B 103 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8322 (pp30) REVERT: B 166 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8188 (mmp80) REVERT: B 252 LYS cc_start: 0.9634 (OUTLIER) cc_final: 0.9407 (ptpp) REVERT: B 265 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8537 (pp) REVERT: B 480 ARG cc_start: 0.9516 (OUTLIER) cc_final: 0.9186 (mtt90) REVERT: Y 100 MET cc_start: 0.9114 (mmm) cc_final: 0.8293 (mmp) REVERT: g 70 MET cc_start: 0.9164 (mtt) cc_final: 0.8834 (mtt) REVERT: g 72 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.7839 (pmt-80) REVERT: g 80 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7445 (p0) REVERT: i 24 LYS cc_start: 0.9402 (tttt) cc_final: 0.9069 (tptm) REVERT: i 27 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8894 (tp40) REVERT: 1 29 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6476 (tp) REVERT: 1 154 TYR cc_start: 0.8804 (p90) cc_final: 0.7955 (p90) REVERT: 2 100 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8648 (p) REVERT: A 95 MET cc_start: 0.9392 (ptm) cc_final: 0.8484 (ppp) REVERT: A 103 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8301 (pp30) REVERT: A 265 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8514 (pp) REVERT: A 480 ARG cc_start: 0.9514 (OUTLIER) cc_final: 0.8910 (mtm110) REVERT: E 656 ASN cc_start: 0.8862 (m-40) cc_final: 0.8625 (t0) REVERT: X 44 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8538 (pm20) REVERT: X 100 MET cc_start: 0.9051 (mmm) cc_final: 0.8695 (mmm) REVERT: f 72 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8672 (pmt-80) REVERT: f 88 MET cc_start: 0.8573 (tmm) cc_final: 0.8049 (tmm) REVERT: h 24 LYS cc_start: 0.9430 (tttt) cc_final: 0.9009 (tptm) REVERT: h 27 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8996 (tp40) REVERT: C 95 MET cc_start: 0.9361 (ptm) cc_final: 0.9074 (ppp) REVERT: C 103 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8549 (tm-30) REVERT: C 166 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8150 (mmp80) REVERT: C 252 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9333 (ptpp) REVERT: C 265 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8436 (pp) REVERT: C 480 ARG cc_start: 0.9528 (OUTLIER) cc_final: 0.9207 (mtt90) REVERT: D 601 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8558 (ttpp) REVERT: H 154 TYR cc_start: 0.8734 (p90) cc_final: 0.7892 (p90) REVERT: L 100 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8664 (p) REVERT: M 100 MET cc_start: 0.9069 (mmm) cc_final: 0.8346 (mmm) REVERT: Q 72 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.7838 (pmt-80) REVERT: Q 88 MET cc_start: 0.8487 (tmm) cc_final: 0.7945 (tmm) REVERT: R 24 LYS cc_start: 0.9339 (tttt) cc_final: 0.9032 (tptm) REVERT: R 27 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.9031 (tp40) outliers start: 185 outliers final: 148 residues processed: 306 average time/residue: 0.2322 time to fit residues: 117.5258 Evaluate side-chains 296 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 123 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 184 LEU Chi-restraints excluded: chain 4 residue 185 THR Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 37 VAL Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 27 GLN Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 1 residue 29 ILE Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 185 THR Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 374 HIS Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 142 ASP Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 100 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 chunk 315 optimal weight: 6.9990 chunk 84 optimal weight: 0.0870 chunk 133 optimal weight: 0.9990 chunk 180 optimal weight: 8.9990 chunk 373 optimal weight: 30.0000 chunk 409 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 376 optimal weight: 8.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 GLN ** 1 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 65 GLN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.053391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.035847 restraints weight = 266123.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.037223 restraints weight = 154424.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037219 restraints weight = 85092.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.037132 restraints weight = 67941.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.037165 restraints weight = 71923.401| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37503 Z= 0.194 Angle : 0.746 14.978 51294 Z= 0.346 Chirality : 0.047 0.414 6096 Planarity : 0.005 0.091 6276 Dihedral : 9.049 87.772 7799 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.24 % Favored : 92.67 % Rotamer: Outliers : 4.64 % Allowed : 20.70 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 4404 helix: 0.58 (0.27), residues: 417 sheet: -0.26 (0.13), residues: 1596 loop : -1.55 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG h 40 TYR 0.013 0.001 TYR C 435 PHE 0.016 0.001 PHE C 288 TRP 0.015 0.001 TRP Y 100J HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00431 (37305) covalent geometry : angle 0.70217 (50754) SS BOND : bond 0.00384 ( 54) SS BOND : angle 1.11691 ( 108) hydrogen bonds : bond 0.03733 ( 1242) hydrogen bonds : angle 5.56898 ( 3384) link_ALPHA1-3 : bond 0.00845 ( 12) link_ALPHA1-3 : angle 1.98330 ( 36) link_ALPHA1-6 : bond 0.00883 ( 6) link_ALPHA1-6 : angle 2.05687 ( 18) link_BETA1-4 : bond 0.00410 ( 75) link_BETA1-4 : angle 2.28093 ( 225) link_NAG-ASN : bond 0.00467 ( 51) link_NAG-ASN : angle 3.58674 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 129 time to evaluate : 1.479 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: 3 154 TYR cc_start: 0.8876 (p90) cc_final: 0.8317 (p90) REVERT: B 95 MET cc_start: 0.9184 (ptm) cc_final: 0.8144 (ppp) REVERT: B 103 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8288 (pp30) REVERT: B 252 LYS cc_start: 0.9635 (OUTLIER) cc_final: 0.9412 (ptpp) REVERT: B 265 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8517 (pp) REVERT: B 480 ARG cc_start: 0.9451 (OUTLIER) cc_final: 0.9068 (mtt90) REVERT: F 654 GLU cc_start: 0.9283 (tp30) cc_final: 0.8658 (pt0) REVERT: F 656 ASN cc_start: 0.8863 (m-40) cc_final: 0.8615 (t0) REVERT: g 70 MET cc_start: 0.9178 (mtt) cc_final: 0.8837 (mtt) REVERT: g 72 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.7850 (pmt-80) REVERT: g 80 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7351 (p0) REVERT: i 24 LYS cc_start: 0.9412 (tttt) cc_final: 0.9058 (tptm) REVERT: i 27 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8876 (tp40) REVERT: 1 29 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6482 (tp) REVERT: 1 154 TYR cc_start: 0.8843 (p90) cc_final: 0.8134 (p90) REVERT: 2 100 VAL cc_start: 0.8967 (OUTLIER) cc_final: 0.8646 (p) REVERT: A 95 MET cc_start: 0.9384 (ptm) cc_final: 0.8480 (ppp) REVERT: A 103 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8390 (pp30) REVERT: A 265 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8501 (pp) REVERT: A 480 ARG cc_start: 0.9488 (OUTLIER) cc_final: 0.8845 (mtm110) REVERT: E 656 ASN cc_start: 0.8860 (m-40) cc_final: 0.8648 (t0) REVERT: X 44 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8600 (pm20) REVERT: X 100 MET cc_start: 0.9020 (mmm) cc_final: 0.8701 (mmm) REVERT: Z 100 GLU cc_start: 0.8744 (tp30) cc_final: 0.8523 (tp30) REVERT: f 72 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.8734 (pmt-80) REVERT: f 88 MET cc_start: 0.8653 (tmm) cc_final: 0.8097 (tmm) REVERT: h 27 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8990 (tp40) REVERT: C 44 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8818 (m) REVERT: C 95 MET cc_start: 0.9312 (ptm) cc_final: 0.9076 (ppp) REVERT: C 103 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: C 265 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8438 (pp) REVERT: C 480 ARG cc_start: 0.9500 (OUTLIER) cc_final: 0.9219 (mtt90) REVERT: D 542 ARG cc_start: 0.9041 (ttm110) cc_final: 0.8801 (ttp-110) REVERT: D 601 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8601 (ttpp) REVERT: D 656 ASN cc_start: 0.8933 (m-40) cc_final: 0.8718 (t0) REVERT: H 154 TYR cc_start: 0.8724 (p90) cc_final: 0.7959 (p90) REVERT: L 100 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8684 (p) REVERT: L 184 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7209 (pt) REVERT: M 100 MET cc_start: 0.9044 (mmm) cc_final: 0.8450 (mmm) REVERT: Q 72 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.7622 (pmt-80) REVERT: Q 88 MET cc_start: 0.8509 (tmm) cc_final: 0.7931 (tmm) REVERT: R 24 LYS cc_start: 0.9358 (tttt) cc_final: 0.9049 (tptm) REVERT: R 27 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.9027 (tp40) outliers start: 179 outliers final: 144 residues processed: 300 average time/residue: 0.2209 time to fit residues: 111.3038 Evaluate side-chains 290 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 122 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 3 residue 206 ASN Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 185 THR Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 65 GLN Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 27 GLN Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 1 residue 29 ILE Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 1 residue 219 ARG Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 185 THR Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain f residue 65 GLN Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 355 optimal weight: 10.0000 chunk 332 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 424 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 GLN ** 1 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN f 65 GLN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.053319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.036265 restraints weight = 266487.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.037259 restraints weight = 149506.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.037204 restraints weight = 89739.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.037327 restraints weight = 79495.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037254 restraints weight = 72147.070| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37503 Z= 0.196 Angle : 0.752 14.783 51294 Z= 0.349 Chirality : 0.047 0.419 6096 Planarity : 0.005 0.091 6276 Dihedral : 9.007 87.907 7797 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.88 % Favored : 92.05 % Rotamer: Outliers : 4.72 % Allowed : 20.83 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 4404 helix: 0.55 (0.27), residues: 417 sheet: -0.23 (0.13), residues: 1587 loop : -1.53 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG R 40 TYR 0.013 0.001 TYR 1 203 PHE 0.018 0.001 PHE B 53 TRP 0.016 0.001 TRP Y 100J HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00434 (37305) covalent geometry : angle 0.70904 (50754) SS BOND : bond 0.00388 ( 54) SS BOND : angle 1.12026 ( 108) hydrogen bonds : bond 0.03788 ( 1242) hydrogen bonds : angle 5.56720 ( 3384) link_ALPHA1-3 : bond 0.00801 ( 12) link_ALPHA1-3 : angle 1.98818 ( 36) link_ALPHA1-6 : bond 0.00830 ( 6) link_ALPHA1-6 : angle 2.01335 ( 18) link_BETA1-4 : bond 0.00400 ( 75) link_BETA1-4 : angle 2.28477 ( 225) link_NAG-ASN : bond 0.00487 ( 51) link_NAG-ASN : angle 3.59195 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8808 Ramachandran restraints generated. 4404 Oldfield, 0 Emsley, 4404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 123 time to evaluate : 1.326 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: 3 154 TYR cc_start: 0.8850 (p90) cc_final: 0.7799 (p90) REVERT: B 95 MET cc_start: 0.9175 (ptm) cc_final: 0.8167 (ppp) REVERT: B 103 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8282 (pp30) REVERT: B 252 LYS cc_start: 0.9640 (OUTLIER) cc_final: 0.9423 (ptpp) REVERT: B 265 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8520 (pp) REVERT: B 480 ARG cc_start: 0.9453 (OUTLIER) cc_final: 0.9069 (mtt90) REVERT: B 501 CYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7405 (p) REVERT: F 656 ASN cc_start: 0.8777 (m-40) cc_final: 0.8532 (t0) REVERT: Y 100 MET cc_start: 0.9084 (mmp) cc_final: 0.8414 (mmm) REVERT: g 70 MET cc_start: 0.9147 (mtt) cc_final: 0.8831 (mtt) REVERT: g 72 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.7880 (pmt-80) REVERT: g 80 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7435 (p0) REVERT: i 24 LYS cc_start: 0.9417 (tttt) cc_final: 0.9053 (tptm) REVERT: i 27 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8903 (tp40) REVERT: 1 29 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6453 (tp) REVERT: 1 154 TYR cc_start: 0.8861 (p90) cc_final: 0.8061 (p90) REVERT: 2 100 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8615 (p) REVERT: A 95 MET cc_start: 0.9394 (ptm) cc_final: 0.8488 (ppp) REVERT: A 103 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8385 (pp30) REVERT: A 265 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8510 (pp) REVERT: A 480 ARG cc_start: 0.9489 (OUTLIER) cc_final: 0.8867 (mtm110) REVERT: E 530 MET cc_start: 0.9344 (tpp) cc_final: 0.8820 (mmp) REVERT: X 44 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8609 (pm20) REVERT: X 100 MET cc_start: 0.9015 (mmm) cc_final: 0.8686 (mmm) REVERT: Z 100 GLU cc_start: 0.8725 (tp30) cc_final: 0.8516 (tp30) REVERT: f 72 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.8712 (pmt-80) REVERT: f 88 MET cc_start: 0.8692 (tmm) cc_final: 0.8145 (tmm) REVERT: h 27 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.9001 (tp40) REVERT: C 95 MET cc_start: 0.9305 (ptm) cc_final: 0.8565 (ppp) REVERT: C 103 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8487 (tm-30) REVERT: C 265 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8442 (pp) REVERT: C 480 ARG cc_start: 0.9506 (OUTLIER) cc_final: 0.9198 (mtt90) REVERT: D 542 ARG cc_start: 0.9039 (ttm110) cc_final: 0.8803 (ttp-110) REVERT: D 601 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8582 (ttpt) REVERT: H 154 TYR cc_start: 0.8718 (p90) cc_final: 0.7847 (p90) REVERT: L 100 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8677 (p) REVERT: L 184 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7117 (pt) REVERT: M 100 MET cc_start: 0.9061 (mmm) cc_final: 0.8503 (mmm) REVERT: Q 72 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.7619 (pmt-80) REVERT: Q 88 MET cc_start: 0.8497 (tmm) cc_final: 0.7942 (tmm) REVERT: R 24 LYS cc_start: 0.9358 (tttt) cc_final: 0.9016 (tptm) REVERT: R 27 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.9037 (tp40) outliers start: 182 outliers final: 151 residues processed: 296 average time/residue: 0.2057 time to fit residues: 102.2219 Evaluate side-chains 293 residues out of total 3858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 118 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 12 VAL Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 159 VAL Chi-restraints excluded: chain 3 residue 178 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 49 ILE Chi-restraints excluded: chain 4 residue 100 VAL Chi-restraints excluded: chain 4 residue 185 THR Chi-restraints excluded: chain 4 residue 194 SER Chi-restraints excluded: chain 4 residue 206 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 103 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 374 HIS Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 480 ARG Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Y residue 63 LEU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 109 VAL Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 63 SER Chi-restraints excluded: chain g residue 11 ILE Chi-restraints excluded: chain g residue 13 THR Chi-restraints excluded: chain g residue 58 VAL Chi-restraints excluded: chain g residue 65 GLN Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 72 ARG Chi-restraints excluded: chain g residue 79 ASP Chi-restraints excluded: chain g residue 80 ASP Chi-restraints excluded: chain g residue 122 GLN Chi-restraints excluded: chain i residue 27 GLN Chi-restraints excluded: chain 1 residue 4 LEU Chi-restraints excluded: chain 1 residue 29 ILE Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 116 VAL Chi-restraints excluded: chain 1 residue 159 VAL Chi-restraints excluded: chain 1 residue 178 VAL Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 206 ASN Chi-restraints excluded: chain 1 residue 219 ARG Chi-restraints excluded: chain 2 residue 20 ILE Chi-restraints excluded: chain 2 residue 23 THR Chi-restraints excluded: chain 2 residue 49 ILE Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 185 THR Chi-restraints excluded: chain 2 residue 206 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 480 ARG Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain E residue 515 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 587 LEU Chi-restraints excluded: chain X residue 4 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain X residue 67 VAL Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 109 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 63 SER Chi-restraints excluded: chain f residue 71 THR Chi-restraints excluded: chain f residue 72 ARG Chi-restraints excluded: chain f residue 79 ASP Chi-restraints excluded: chain h residue 27 GLN Chi-restraints excluded: chain h residue 72 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 445 CYS Chi-restraints excluded: chain C residue 480 ARG Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 44 GLN Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 72 ARG Chi-restraints excluded: chain Q residue 79 ASP Chi-restraints excluded: chain Q residue 122 GLN Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 14 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 380 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 256 optimal weight: 7.9990 chunk 428 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 363 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 GLN ** 1 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN f 65 GLN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.052799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.034969 restraints weight = 266102.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.035594 restraints weight = 152007.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.035865 restraints weight = 109553.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.036160 restraints weight = 79651.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.036190 restraints weight = 70134.437| |-----------------------------------------------------------------------------| r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 37503 Z= 0.251 Angle : 0.795 14.382 51294 Z= 0.370 Chirality : 0.048 0.431 6096 Planarity : 0.005 0.093 6276 Dihedral : 9.165 88.754 7797 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.17 % Favored : 91.73 % Rotamer: Outliers : 4.98 % Allowed : 20.73 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.12), residues: 4404 helix: 0.40 (0.26), residues: 417 sheet: -0.27 (0.13), residues: 1557 loop : -1.59 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 40 TYR 0.014 0.001 TYR C 435 PHE 0.018 0.002 PHE C 288 TRP 0.017 0.002 TRP A 427 HIS 0.006 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00555 (37305) covalent geometry : angle 0.75302 (50754) SS BOND : bond 0.00412 ( 54) SS BOND : angle 1.18162 ( 108) hydrogen bonds : bond 0.04063 ( 1242) hydrogen bonds : angle 5.69403 ( 3384) link_ALPHA1-3 : bond 0.00737 ( 12) link_ALPHA1-3 : angle 2.02429 ( 36) link_ALPHA1-6 : bond 0.00761 ( 6) link_ALPHA1-6 : angle 1.99592 ( 18) link_BETA1-4 : bond 0.00400 ( 75) link_BETA1-4 : angle 2.33090 ( 225) link_NAG-ASN : bond 0.00529 ( 51) link_NAG-ASN : angle 3.67909 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6235.55 seconds wall clock time: 109 minutes 15.39 seconds (6555.39 seconds total)