Starting phenix.real_space_refine on Fri Feb 6 17:07:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yqo_73342/02_2026/9yqo_73342.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yqo_73342/02_2026/9yqo_73342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yqo_73342/02_2026/9yqo_73342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yqo_73342/02_2026/9yqo_73342.map" model { file = "/net/cci-nas-00/data/ceres_data/9yqo_73342/02_2026/9yqo_73342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yqo_73342/02_2026/9yqo_73342.cif" } resolution = 3.26 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= 0.000 sd= 0.040 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 153 5.16 5 C 16500 2.51 5 N 4347 2.21 5 O 5433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26433 Number of models: 1 Model: "" Number of chains: 69 Chain: "M" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "N" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "Q" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "R" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1020 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "A" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3540 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "B" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1040 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "D" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "F" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1020 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "G" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3540 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "H" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1040 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "J" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 791 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 96} Chain: "L" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1020 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "O" Number of atoms: 3540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3540 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 2 Chain: "P" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1040 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: 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: "V" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "W" 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: "X" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "Y" 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: "Z" 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: "a" 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: "b" 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: "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: 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: "e" 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: "f" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "g" 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 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: "k" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "l" 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: "m" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: 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: 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: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 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: "x" 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: "y" 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: "z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.84, per 1000 atoms: 0.26 Number of scatterers: 26433 At special positions: 0 Unit cell: (159.154, 154.938, 152.83, 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 153 16.00 O 5433 8.00 N 4347 7.00 C 16500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 32 " - pdb=" SG CYS M 98 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 92 " distance=2.11 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.14 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.14 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.05 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=2.03 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 A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.05 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.14 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.02 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.16 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.13 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS H 605 " distance=2.03 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.06 Simple disulfide: pdb=" SG CYS I 32 " - pdb=" SG CYS I 98 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.14 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.12 Simple disulfide: pdb=" SG CYS O 54 " - pdb=" SG CYS O 74 " distance=2.02 Simple disulfide: pdb=" SG CYS O 119 " - pdb=" SG CYS O 205 " distance=2.14 Simple disulfide: pdb=" SG CYS O 126 " - pdb=" SG CYS O 196 " distance=2.09 Simple disulfide: pdb=" SG CYS O 131 " - pdb=" SG CYS O 157 " distance=2.03 Simple disulfide: pdb=" SG CYS O 218 " - pdb=" SG CYS O 247 " distance=2.03 Simple disulfide: pdb=" SG CYS O 228 " - pdb=" SG CYS O 239 " distance=2.03 Simple disulfide: pdb=" SG CYS O 296 " - pdb=" SG CYS O 331 " distance=2.03 Simple disulfide: pdb=" SG CYS O 378 " - pdb=" SG CYS O 445 " distance=2.03 Simple disulfide: pdb=" SG CYS O 385 " - pdb=" SG CYS O 418 " distance=2.04 Simple disulfide: pdb=" SG CYS O 501 " - pdb=" SG CYS P 605 " distance=2.03 Simple disulfide: pdb=" SG CYS P 598 " - pdb=" SG CYS P 604 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 1 4 " - " MAN 1 5 " " MAN 1 5 " - " MAN 1 6 " " MAN V 4 " - " MAN V 5 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN k 4 " - " MAN k 5 " " MAN m 4 " - " MAN m 5 " " MAN m 5 " - " MAN m 6 " " MAN z 4 " - " MAN z 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " MAN 1 7 " - " MAN 1 8 " " MAN 9 4 " - " MAN 9 5 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " MAN X 7 " - " MAN X 8 " " MAN f 4 " - " MAN f 5 " " BMA k 3 " - " MAN k 4 " " BMA m 3 " - " MAN m 4 " " MAN m 7 " - " MAN m 8 " " MAN u 4 " - " MAN u 5 " " BMA z 3 " - " MAN z 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 7 " " MAN 1 7 " - " MAN 1 9 " " BMA 9 3 " - " MAN 9 4 " " MAN 9 4 " - " MAN 9 6 " " BMA V 3 " - " MAN V 6 " " BMA X 3 " - " MAN X 7 " " MAN X 7 " - " MAN X 9 " " BMA f 3 " - " MAN f 4 " " MAN f 4 " - " MAN f 6 " " BMA k 3 " - " MAN k 6 " " BMA m 3 " - " MAN m 7 " " MAN m 7 " - " MAN m 9 " " BMA u 3 " - " MAN u 4 " " MAN u 4 " - " MAN u 6 " " BMA z 3 " - " MAN z 6 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " 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 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " " NAGAA 1 " - " NAGAA 2 " NAG-ASN " NAG 0 1 " - " ASN O 301 " " NAG 1 1 " - " ASN O 332 " " NAG 2 1 " - " ASN O 362 " " NAG 3 1 " - " ASN O 386 " " NAG 4 1 " - " ASN O 392 " " NAG 5 1 " - " ASN O 448 " " NAG 6 1 " - " ASN O 197 " " NAG 7 1 " - " ASN O 241 " " NAG 8 1 " - " ASN O 295 " " NAG 9 1 " - " ASN O 276 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 289 " " NAG A 603 " - " ASN A 339 " " NAG A 604 " - " ASN A 356 " " NAG A 605 " - " ASN A 396 " " NAG B 701 " - " ASN B 625 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 289 " " NAG G 603 " - " ASN G 339 " " NAG G 604 " - " ASN G 356 " " NAG G 605 " - " ASN G 396 " " NAG H 701 " - " ASN H 625 " " NAG O 601 " - " ASN O 88 " " NAG O 602 " - " ASN O 289 " " NAG O 603 " - " ASN O 339 " " NAG O 604 " - " ASN O 356 " " NAG O 605 " - " ASN O 396 " " NAG P 701 " - " ASN P 625 " " NAG S 1 " - " ASN N 72 " " NAG T 1 " - " ASN A 130 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 262 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN A 362 " " NAG Z 1 " - " ASN A 386 " " NAG a 1 " - " ASN A 392 " " NAG b 1 " - " ASN A 448 " " NAG c 1 " - " ASN A 197 " " NAG d 1 " - " ASN A 241 " " NAG e 1 " - " ASN A 295 " " NAG f 1 " - " ASN A 276 " " NAG g 1 " - " ASN A 160 " " NAG h 1 " - " ASN D 72 " " NAG i 1 " - " ASN G 130 " " NAG j 1 " - " ASN G 156 " " NAG k 1 " - " ASN G 262 " " NAG l 1 " - " ASN G 301 " " NAG m 1 " - " ASN G 332 " " NAG n 1 " - " ASN G 362 " " NAG o 1 " - " ASN G 386 " " NAG p 1 " - " ASN G 392 " " NAG q 1 " - " ASN G 448 " " NAG r 1 " - " ASN G 197 " " NAG s 1 " - " ASN G 241 " " NAG t 1 " - " ASN G 295 " " NAG u 1 " - " ASN G 276 " " NAG v 1 " - " ASN G 160 " " NAG w 1 " - " ASN J 72 " " NAG x 1 " - " ASN O 130 " " NAG y 1 " - " ASN O 156 " " NAG z 1 " - " ASN O 262 " " NAGAA 1 " - " ASN O 160 " Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 49 sheets defined 19.9% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.624A pdb=" N CYS M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.520A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.989A pdb=" N SER R 32 " --> pdb=" O ILE R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 87 Processing helix chain 'R' and resid 100D through 100H Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.169A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.801A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 520 Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.656A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 568 through 596 removed outlier: 3.897A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.555A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.609A pdb=" N CYS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.578A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.988A pdb=" N SER F 32 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 100D through 100H Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 98 through 116 removed outlier: 4.176A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 390 Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.825A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 520 Processing helix chain 'H' and resid 529 through 534 removed outlier: 3.618A pdb=" N SER H 534 " --> pdb=" O MET H 530 " (cutoff:3.500A) Processing helix chain 'H' and resid 536 through 542 Processing helix chain 'H' and resid 568 through 596 removed outlier: 3.870A pdb=" N LYS H 574 " --> pdb=" O VAL H 570 " (cutoff:3.500A) Processing helix chain 'H' and resid 618 through 625 Processing helix chain 'H' and resid 627 through 635 Processing helix chain 'H' and resid 638 through 664 removed outlier: 3.543A pdb=" N ASN H 651 " --> pdb=" O GLU H 647 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.651A pdb=" N CYS I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.568A pdb=" N PHE J 83 " --> pdb=" O SER J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.988A pdb=" N SER L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 100D through 100H Processing helix chain 'O' and resid 70 through 74 Processing helix chain 'O' and resid 98 through 117 removed outlier: 4.172A pdb=" N GLU O 102 " --> pdb=" O ASN O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 126 Processing helix chain 'O' and resid 335 through 353 Processing helix chain 'O' and resid 368 through 373 Processing helix chain 'O' and resid 387 through 390 Processing helix chain 'O' and resid 396 through 405 Processing helix chain 'O' and resid 475 through 484 removed outlier: 3.782A pdb=" N SER O 481 " --> pdb=" O ASP O 477 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU O 482 " --> pdb=" O ASN O 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 516 through 520 Processing helix chain 'P' and resid 529 through 534 removed outlier: 3.661A pdb=" N SER P 534 " --> pdb=" O MET P 530 " (cutoff:3.500A) Processing helix chain 'P' and resid 536 through 542 Processing helix chain 'P' and resid 568 through 596 removed outlier: 3.913A pdb=" N LYS P 574 " --> pdb=" O VAL P 570 " (cutoff:3.500A) Processing helix chain 'P' and resid 618 through 625 Processing helix chain 'P' and resid 627 through 635 Processing helix chain 'P' and resid 638 through 664 removed outlier: 3.597A pdb=" N ASN P 651 " --> pdb=" O GLU P 647 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'M' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 12 current: chain 'M' and resid 46 through 52 removed outlier: 4.216A pdb=" N ALA M 56 " --> pdb=" O LYS M 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 56 through 59 current: chain 'M' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AA4, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.521A pdb=" N TRP N 35 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 12 through 13 removed outlier: 4.778A pdb=" N TYR Q 86 " --> pdb=" O GLY Q 101 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR Q 103 " --> pdb=" O ALA Q 84 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA Q 84 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP Q 35 " --> pdb=" O ILE Q 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 19 through 22 Processing sheet with id=AA7, first strand: chain 'R' and resid 3 through 7 removed outlier: 4.667A pdb=" N GLU R 16 " --> pdb=" O ALA R 82B" (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA R 82B" --> pdb=" O GLU R 16 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 11 through 12 current: chain 'R' and resid 44 through 47 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 44 through 47 current: chain 'R' and resid 100J through 100O No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.389A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.667A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AB3, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.947A pdb=" N ARG A 66 " --> pdb=" O THR A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.002A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 308 removed outlier: 6.723A pdb=" N ASN A 301 " --> pdb=" O ILE A 322A" (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A 322A" --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 316 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB9, first strand: chain 'C' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 10 through 12 current: chain 'C' and resid 46 through 52 removed outlier: 4.198A pdb=" N ALA C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 59 current: chain 'C' and resid 102 through 103 Processing sheet with id=AC1, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.517A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 12 through 13 removed outlier: 4.761A pdb=" N TYR E 86 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N THR E 103 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA E 84 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP E 35 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 22 Processing sheet with id=AC5, first strand: chain 'F' and resid 3 through 7 removed outlier: 4.519A pdb=" N GLU F 16 " --> pdb=" O ALA F 82B" (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA F 82B" --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 33 through 40 removed outlier: 3.551A pdb=" N SER F 40 " --> pdb=" O GLY F 44 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 44 through 47 current: chain 'F' and resid 100J through 101 Processing sheet with id=AC7, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.381A pdb=" N VAL H 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL G 38 " --> pdb=" O THR H 606 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR H 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR G 40 " --> pdb=" O CYS H 604 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N CYS H 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AD1, first strand: chain 'G' and resid 66 through 67 removed outlier: 6.761A pdb=" N ARG G 66 " --> pdb=" O THR G 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AD4, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.036A pdb=" N VAL G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N TYR G 435 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 259 through 261 current: chain 'G' and resid 284 through 312 removed outlier: 6.708A pdb=" N ASN G 301 " --> pdb=" O ILE G 322A" (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE G 322A" --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 315 through 323 current: chain 'G' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 381 through 385 current: chain 'G' and resid 465 through 470 Processing sheet with id=AD6, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 46 through 52 removed outlier: 4.121A pdb=" N ALA I 56 " --> pdb=" O LYS I 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 56 through 59 current: chain 'I' and resid 102 through 103 Processing sheet with id=AD8, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.508A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 12 through 13 removed outlier: 5.257A pdb=" N TYR K 86 " --> pdb=" O GLY K 101 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR K 103 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA K 84 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 19 through 22 Processing sheet with id=AE3, first strand: chain 'L' and resid 3 through 7 removed outlier: 4.444A pdb=" N GLU L 16 " --> pdb=" O ALA L 82B" (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA L 82B" --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 33 through 40 removed outlier: 6.787A pdb=" N TRP L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR L 50 " --> pdb=" O TRP L 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N TRP L 36 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER L 40 " --> pdb=" O GLY L 44 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 44 through 51 current: chain 'L' and resid 100J through 100O Processing sheet with id=AE5, first strand: chain 'O' and resid 494 through 499 removed outlier: 5.384A pdb=" N VAL P 608 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N VAL O 38 " --> pdb=" O THR P 606 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR P 606 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR O 40 " --> pdb=" O CYS P 604 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N CYS P 604 " --> pdb=" O TYR O 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 45 through 47 removed outlier: 3.685A pdb=" N ILE O 225 " --> pdb=" O VAL O 245 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL O 242 " --> pdb=" O LEU O 86 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 75 through 76 Processing sheet with id=AE8, first strand: chain 'O' and resid 66 through 67 removed outlier: 6.957A pdb=" N ARG O 66 " --> pdb=" O THR O 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'O' and resid 91 through 94 Processing sheet with id=AF1, first strand: chain 'O' and resid 154 through 162 Processing sheet with id=AF2, first strand: chain 'O' and resid 181 through 183 Processing sheet with id=AF3, first strand: chain 'O' and resid 200 through 203 removed outlier: 6.041A pdb=" N VAL O 200 " --> pdb=" O ALA O 433 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR O 435 " --> pdb=" O VAL O 200 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR O 202 " --> pdb=" O TYR O 435 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 259 through 261 current: chain 'O' and resid 284 through 312 removed outlier: 6.721A pdb=" N ASN O 301 " --> pdb=" O ILE O 322A" (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE O 322A" --> pdb=" O ASN O 301 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR O 303 " --> pdb=" O GLY O 321 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG O 315 " --> pdb=" O ILE O 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 315 through 323 current: chain 'O' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 381 through 385 current: chain 'O' and resid 465 through 470 767 hydrogen bonds defined for protein. 1935 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: 5.37 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4698 1.32 - 1.45: 7586 1.45 - 1.58: 14485 1.58 - 1.71: 0 1.71 - 1.84: 210 Bond restraints: 26979 Sorted by residual: bond pdb=" CD GLU N 96 " pdb=" OE1 GLU N 96 " ideal model delta sigma weight residual 1.249 1.191 0.058 1.90e-02 2.77e+03 9.27e+00 bond pdb=" CG ASP G 167 " pdb=" OD1 ASP G 167 " ideal model delta sigma weight residual 1.249 1.192 0.057 1.90e-02 2.77e+03 9.13e+00 bond pdb=" CG ASP O 167 " pdb=" OD1 ASP O 167 " ideal model delta sigma weight residual 1.249 1.193 0.056 1.90e-02 2.77e+03 8.66e+00 bond pdb=" CG ASP A 167 " pdb=" OD1 ASP A 167 " ideal model delta sigma weight residual 1.249 1.195 0.054 1.90e-02 2.77e+03 8.18e+00 bond pdb=" CG GLU N 96 " pdb=" CD GLU N 96 " ideal model delta sigma weight residual 1.516 1.445 0.071 2.50e-02 1.60e+03 8.07e+00 ... (remaining 26974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 32230 1.77 - 3.53: 3678 3.53 - 5.30: 586 5.30 - 7.07: 146 7.07 - 8.83: 11 Bond angle restraints: 36651 Sorted by residual: angle pdb=" C LYS I 52 " pdb=" N PRO I 52A" pdb=" CA PRO I 52A" ideal model delta sigma weight residual 119.56 128.39 -8.83 1.02e+00 9.61e-01 7.50e+01 angle pdb=" C LYS C 52 " pdb=" N PRO C 52A" pdb=" CA PRO C 52A" ideal model delta sigma weight residual 119.56 128.22 -8.66 1.02e+00 9.61e-01 7.21e+01 angle pdb=" C LYS M 52 " pdb=" N PRO M 52A" pdb=" CA PRO M 52A" ideal model delta sigma weight residual 119.56 128.05 -8.49 1.02e+00 9.61e-01 6.93e+01 angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 125.07 -5.41 7.20e-01 1.93e+00 5.65e+01 angle pdb=" C GLU G 492 " pdb=" N PRO G 493 " pdb=" CA PRO G 493 " ideal model delta sigma weight residual 119.56 127.08 -7.52 1.01e+00 9.80e-01 5.55e+01 ... (remaining 36646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.22: 17433 21.22 - 42.45: 410 42.45 - 63.67: 96 63.67 - 84.90: 104 84.90 - 106.12: 50 Dihedral angle restraints: 18093 sinusoidal: 9201 harmonic: 8892 Sorted by residual: dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 33.24 59.76 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 92 " pdb=" CB CYS L 92 " ideal model delta sinusoidal sigma weight residual 93.00 37.36 55.64 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS R 22 " pdb=" SG CYS R 22 " pdb=" SG CYS R 92 " pdb=" CB CYS R 92 " ideal model delta sinusoidal sigma weight residual 93.00 44.95 48.05 1 1.00e+01 1.00e-02 3.18e+01 ... (remaining 18090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3721 0.090 - 0.181: 712 0.181 - 0.271: 68 0.271 - 0.362: 8 0.362 - 0.452: 6 Chirality restraints: 4515 Sorted by residual: chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 5.11e+02 chirality pdb=" C1 MAN V 4 " pdb=" O3 BMA V 3 " pdb=" C2 MAN V 4 " pdb=" O5 MAN V 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 5.10e+02 chirality pdb=" C1 MAN z 4 " pdb=" O3 BMA z 3 " pdb=" C2 MAN z 4 " pdb=" O5 MAN z 4 " both_signs ideal model delta sigma weight residual False 2.40 1.95 0.45 2.00e-02 2.50e+03 5.09e+02 ... (remaining 4512 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 664 " 0.030 2.00e-02 2.50e+03 6.14e-02 3.77e+01 pdb=" C ASP B 664 " -0.106 2.00e-02 2.50e+03 pdb=" O ASP B 664 " 0.038 2.00e-02 2.50e+03 pdb=" OXT ASP B 664 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 664 " -0.030 2.00e-02 2.50e+03 6.12e-02 3.75e+01 pdb=" C ASP P 664 " 0.106 2.00e-02 2.50e+03 pdb=" O ASP P 664 " -0.038 2.00e-02 2.50e+03 pdb=" OXT ASP P 664 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 664 " 0.030 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" C ASP H 664 " -0.105 2.00e-02 2.50e+03 pdb=" O ASP H 664 " 0.038 2.00e-02 2.50e+03 pdb=" OXT ASP H 664 " 0.037 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 10744 2.89 - 3.39: 22137 3.39 - 3.90: 44842 3.90 - 4.40: 49387 4.40 - 4.90: 83615 Nonbonded interactions: 210725 Sorted by model distance: nonbonded pdb=" OE1 GLN Q 34 " pdb=" OH TYR Q 36 " model vdw 2.389 3.040 nonbonded pdb=" O3 NAG k 2 " pdb=" O5 BMA k 3 " model vdw 2.397 3.040 nonbonded pdb=" O3 NAG V 2 " pdb=" O5 BMA V 3 " model vdw 2.397 3.040 nonbonded pdb=" O3 NAG z 2 " pdb=" O5 BMA z 3 " model vdw 2.398 3.040 nonbonded pdb=" O3 NAG 9 1 " pdb=" O5 NAG 9 2 " model vdw 2.438 3.040 ... (remaining 210720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '7' selection = chain '8' selection = chain 'AA' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 't' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' } ncs_group { reference = chain '1' selection = chain 'X' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'c' selection = chain 'r' } ncs_group { reference = chain '9' selection = chain 'V' selection = chain 'f' selection = chain 'k' selection = chain 'u' selection = chain 'z' } ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.020 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.013 0.130 27183 Z= 0.673 Angle : 1.386 19.479 37215 Z= 0.829 Chirality : 0.071 0.452 4515 Planarity : 0.005 0.061 4464 Dihedral : 12.933 106.121 12243 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.07 % Allowed : 0.81 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.58 (0.15), residues: 3048 helix: 0.21 (0.21), residues: 435 sheet: 1.47 (0.15), residues: 972 loop : 2.64 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 31 TYR 0.041 0.004 TYR G 40 PHE 0.017 0.003 PHE I 29 TRP 0.044 0.005 TRP F 101 HIS 0.007 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.01186 (26979) covalent geometry : angle 1.23788 (36651) SS BOND : bond 0.04710 ( 48) SS BOND : angle 3.84374 ( 96) hydrogen bonds : bond 0.19142 ( 767) hydrogen bonds : angle 7.80647 ( 1935) link_ALPHA1-2 : bond 0.04673 ( 9) link_ALPHA1-2 : angle 6.03856 ( 27) link_ALPHA1-3 : bond 0.04650 ( 12) link_ALPHA1-3 : angle 4.14226 ( 36) link_ALPHA1-6 : bond 0.03796 ( 15) link_ALPHA1-6 : angle 3.87552 ( 45) link_BETA1-4 : bond 0.04668 ( 57) link_BETA1-4 : angle 7.16367 ( 171) link_NAG-ASN : bond 0.06884 ( 63) link_NAG-ASN : angle 3.86631 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 777 time to evaluate : 1.037 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: M 82 SER cc_start: 0.7758 (m) cc_final: 0.7486 (t) REVERT: N 77 ASN cc_start: 0.7782 (t0) cc_final: 0.7320 (t0) REVERT: Q 26 LYS cc_start: 0.7819 (mttt) cc_final: 0.7594 (mtpt) REVERT: Q 89 HIS cc_start: 0.2492 (t-90) cc_final: 0.2057 (t-170) REVERT: R 34 TRP cc_start: 0.4952 (m100) cc_final: 0.4664 (m100) REVERT: R 97 HIS cc_start: 0.5185 (p90) cc_final: 0.4819 (p-80) REVERT: R 99 ARG cc_start: 0.7995 (ptm160) cc_final: 0.7316 (ptm160) REVERT: R 100 ASN cc_start: 0.8272 (m-40) cc_final: 0.8054 (m-40) REVERT: R 100 MET cc_start: 0.5029 (mtm) cc_final: 0.4496 (mtm) REVERT: B 588 ARG cc_start: 0.8165 (tpt170) cc_final: 0.7688 (ttm170) REVERT: C 82 SER cc_start: 0.7872 (m) cc_final: 0.7651 (t) REVERT: D 45 ARG cc_start: 0.7849 (ptt180) cc_final: 0.7379 (ptp90) REVERT: D 77 ASN cc_start: 0.7675 (t0) cc_final: 0.6939 (t0) REVERT: D 104 VAL cc_start: 0.6705 (t) cc_final: 0.6456 (m) REVERT: E 89 HIS cc_start: 0.1928 (t-90) cc_final: 0.1086 (t-170) REVERT: E 90 ILE cc_start: 0.5429 (mt) cc_final: 0.5020 (pt) REVERT: F 47 TRP cc_start: 0.3794 (t60) cc_final: 0.3515 (t-100) REVERT: F 69 LEU cc_start: 0.3849 (tp) cc_final: 0.3415 (tp) REVERT: F 100 THR cc_start: 0.7039 (m) cc_final: 0.6198 (p) REVERT: F 100 MET cc_start: 0.1441 (ttm) cc_final: -0.0762 (ttm) REVERT: H 588 ARG cc_start: 0.8188 (tpt170) cc_final: 0.7705 (ttm170) REVERT: I 82 SER cc_start: 0.7681 (m) cc_final: 0.7399 (t) REVERT: J 77 ASN cc_start: 0.7851 (t0) cc_final: 0.7228 (t0) REVERT: K 35 TRP cc_start: 0.5634 (m100) cc_final: 0.5345 (m100) REVERT: K 89 HIS cc_start: 0.1916 (t-90) cc_final: 0.1514 (t-170) REVERT: K 96 TRP cc_start: 0.4426 (m100) cc_final: 0.3462 (m100) REVERT: L 80 LEU cc_start: 0.3693 (tp) cc_final: 0.3413 (tt) REVERT: L 97 HIS cc_start: 0.6297 (p90) cc_final: 0.6053 (p90) REVERT: O 411 ASN cc_start: 0.5691 (t0) cc_final: 0.4547 (p0) REVERT: P 588 ARG cc_start: 0.8107 (tpt170) cc_final: 0.7544 (ttm170) outliers start: 2 outliers final: 0 residues processed: 777 average time/residue: 0.2152 time to fit residues: 248.2318 Evaluate side-chains 399 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN A 246 GLN E 34 GLN E 50 ASN F 100HASN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 442 GLN H 616 ASN K 34 GLN K 50 ASN O 280 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.172405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123459 restraints weight = 38951.517| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.39 r_work: 0.3379 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27183 Z= 0.157 Angle : 0.712 21.867 37215 Z= 0.339 Chirality : 0.046 0.233 4515 Planarity : 0.004 0.035 4464 Dihedral : 9.698 75.962 6537 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.15 % Allowed : 8.21 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 2.15 (0.15), residues: 3048 helix: 1.43 (0.25), residues: 438 sheet: 1.14 (0.15), residues: 987 loop : 1.88 (0.16), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 61 TYR 0.021 0.002 TYR R 100M PHE 0.015 0.002 PHE I 29 TRP 0.024 0.002 TRP R 36 HIS 0.005 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00355 (26979) covalent geometry : angle 0.64880 (36651) SS BOND : bond 0.00712 ( 48) SS BOND : angle 1.61054 ( 96) hydrogen bonds : bond 0.05644 ( 767) hydrogen bonds : angle 6.08120 ( 1935) link_ALPHA1-2 : bond 0.00718 ( 9) link_ALPHA1-2 : angle 2.01303 ( 27) link_ALPHA1-3 : bond 0.00995 ( 12) link_ALPHA1-3 : angle 1.32222 ( 36) link_ALPHA1-6 : bond 0.00394 ( 15) link_ALPHA1-6 : angle 1.65373 ( 45) link_BETA1-4 : bond 0.00466 ( 57) link_BETA1-4 : angle 2.41136 ( 171) link_NAG-ASN : bond 0.00352 ( 63) link_NAG-ASN : angle 3.17322 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 445 time to evaluate : 0.991 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: M 69 MET cc_start: 0.8463 (mtt) cc_final: 0.8060 (mtt) REVERT: M 82 SER cc_start: 0.8058 (m) cc_final: 0.7627 (t) REVERT: N 39 ARG cc_start: 0.6601 (mtm110) cc_final: 0.6290 (mpt-90) REVERT: N 42 GLN cc_start: 0.8299 (mt0) cc_final: 0.7928 (pt0) REVERT: N 77 ASN cc_start: 0.7702 (t0) cc_final: 0.7119 (t0) REVERT: Q 87 TYR cc_start: 0.6138 (m-80) cc_final: 0.5873 (m-80) REVERT: R 90 TYR cc_start: 0.6892 (m-80) cc_final: 0.6689 (m-10) REVERT: R 97 HIS cc_start: 0.6500 (p90) cc_final: 0.6133 (p-80) REVERT: R 99 ARG cc_start: 0.8397 (ptm160) cc_final: 0.8126 (ptm160) REVERT: R 100 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7456 (mt-10) REVERT: A 92 ASN cc_start: 0.7992 (m-40) cc_final: 0.7063 (t0) REVERT: A 252 ARG cc_start: 0.8415 (mtt90) cc_final: 0.8028 (mtt-85) REVERT: B 588 ARG cc_start: 0.8160 (tpt170) cc_final: 0.7264 (ttm170) REVERT: C 82 SER cc_start: 0.8073 (m) cc_final: 0.7650 (t) REVERT: D 45 ARG cc_start: 0.8080 (ptt180) cc_final: 0.7128 (ptp90) REVERT: D 70 ASP cc_start: 0.8017 (m-30) cc_final: 0.7760 (m-30) REVERT: D 77 ASN cc_start: 0.7478 (t0) cc_final: 0.6752 (t0) REVERT: F 97 HIS cc_start: 0.6862 (p90) cc_final: 0.6471 (p-80) REVERT: G 92 ASN cc_start: 0.8014 (m-40) cc_final: 0.7063 (t0) REVERT: G 504 ARG cc_start: 0.7722 (tpm170) cc_final: 0.7324 (tpm170) REVERT: H 588 ARG cc_start: 0.8150 (tpt170) cc_final: 0.7245 (ttm170) REVERT: I 82 SER cc_start: 0.7882 (m) cc_final: 0.7442 (t) REVERT: J 45 ARG cc_start: 0.7902 (ptt180) cc_final: 0.7635 (ttp-170) REVERT: J 54 ARG cc_start: 0.7675 (mtt90) cc_final: 0.7205 (mtm-85) REVERT: J 77 ASN cc_start: 0.7822 (t0) cc_final: 0.7024 (t0) REVERT: K 35 TRP cc_start: 0.7883 (m100) cc_final: 0.7645 (m100) REVERT: K 87 TYR cc_start: 0.6303 (m-80) cc_final: 0.5971 (m-80) REVERT: K 92 ASP cc_start: 0.7575 (m-30) cc_final: 0.7218 (m-30) REVERT: L 36 TRP cc_start: 0.5863 (m100) cc_final: 0.5602 (m100) REVERT: L 99 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7594 (ttm170) REVERT: L 100 MET cc_start: 0.5842 (mtt) cc_final: 0.5344 (mpp) REVERT: O 92 ASN cc_start: 0.8110 (m-40) cc_final: 0.7142 (t0) REVERT: O 99 ASN cc_start: 0.8014 (t0) cc_final: 0.7489 (m-40) REVERT: O 411 ASN cc_start: 0.5745 (t0) cc_final: 0.4368 (p0) REVERT: P 588 ARG cc_start: 0.8174 (tpt170) cc_final: 0.7167 (ttm170) REVERT: P 628 TRP cc_start: 0.7600 (m100) cc_final: 0.7325 (m100) outliers start: 58 outliers final: 34 residues processed: 477 average time/residue: 0.1916 time to fit residues: 140.9165 Evaluate side-chains 397 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 362 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 88 CYS Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 100 GLU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 520 LEU Chi-restraints excluded: chain H residue 584 GLU Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain O residue 196 CYS Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 637 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 153 optimal weight: 0.0980 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 50 ASN ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 616 ASN O 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.169865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129048 restraints weight = 38457.107| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 3.61 r_work: 0.3335 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27183 Z= 0.164 Angle : 0.655 18.068 37215 Z= 0.313 Chirality : 0.045 0.187 4515 Planarity : 0.004 0.035 4464 Dihedral : 8.741 79.345 6537 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.89 % Allowed : 9.47 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.15), residues: 3048 helix: 1.35 (0.25), residues: 438 sheet: 1.06 (0.15), residues: 969 loop : 1.38 (0.16), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 53 TYR 0.021 0.002 TYR M 59 PHE 0.016 0.002 PHE N 98 TRP 0.034 0.002 TRP R 36 HIS 0.005 0.001 HIS O 105 Details of bonding type rmsd covalent geometry : bond 0.00381 (26979) covalent geometry : angle 0.59844 (36651) SS BOND : bond 0.00457 ( 48) SS BOND : angle 1.55031 ( 96) hydrogen bonds : bond 0.04698 ( 767) hydrogen bonds : angle 5.66224 ( 1935) link_ALPHA1-2 : bond 0.00733 ( 9) link_ALPHA1-2 : angle 1.85843 ( 27) link_ALPHA1-3 : bond 0.00961 ( 12) link_ALPHA1-3 : angle 1.39132 ( 36) link_ALPHA1-6 : bond 0.00416 ( 15) link_ALPHA1-6 : angle 1.71769 ( 45) link_BETA1-4 : bond 0.00441 ( 57) link_BETA1-4 : angle 2.15906 ( 171) link_NAG-ASN : bond 0.00270 ( 63) link_NAG-ASN : angle 2.81684 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 396 time to evaluate : 0.987 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: M 69 MET cc_start: 0.8633 (mtt) cc_final: 0.8036 (mtt) REVERT: M 72 ASP cc_start: 0.8469 (t70) cc_final: 0.8215 (t70) REVERT: M 82 SER cc_start: 0.8139 (m) cc_final: 0.7714 (t) REVERT: N 77 ASN cc_start: 0.7795 (t0) cc_final: 0.7203 (t0) REVERT: Q 31 ARG cc_start: 0.6983 (ptp90) cc_final: 0.6289 (ptp-170) REVERT: Q 33 VAL cc_start: 0.6155 (t) cc_final: 0.5859 (t) REVERT: Q 35 TRP cc_start: 0.7734 (m100) cc_final: 0.7326 (m100) REVERT: A 92 ASN cc_start: 0.7991 (m-40) cc_final: 0.7194 (t0) REVERT: A 205 CYS cc_start: 0.6459 (OUTLIER) cc_final: 0.5923 (m) REVERT: A 252 ARG cc_start: 0.8422 (mtt90) cc_final: 0.8011 (mtt-85) REVERT: A 504 ARG cc_start: 0.7642 (tpm170) cc_final: 0.7220 (tpm170) REVERT: B 588 ARG cc_start: 0.8119 (tpt170) cc_final: 0.7258 (ttm170) REVERT: C 82 SER cc_start: 0.8162 (m) cc_final: 0.7722 (t) REVERT: D 45 ARG cc_start: 0.8025 (ptt180) cc_final: 0.7134 (ptp90) REVERT: D 77 ASN cc_start: 0.7507 (t0) cc_final: 0.6839 (t0) REVERT: D 79 GLU cc_start: 0.4500 (mp0) cc_final: 0.4176 (mp0) REVERT: E 26 LYS cc_start: 0.7764 (mtmm) cc_final: 0.7527 (mtpt) REVERT: E 50 ASN cc_start: 0.5456 (t0) cc_final: 0.4929 (t0) REVERT: E 91 TRP cc_start: 0.8284 (m100) cc_final: 0.8074 (m100) REVERT: F 36 TRP cc_start: 0.6382 (m100) cc_final: 0.5825 (m100) REVERT: F 47 TRP cc_start: 0.6520 (t-100) cc_final: 0.5611 (t-100) REVERT: F 100 PHE cc_start: 0.5393 (t80) cc_final: 0.4974 (t80) REVERT: G 92 ASN cc_start: 0.7996 (m-40) cc_final: 0.7034 (t0) REVERT: G 205 CYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6011 (m) REVERT: G 504 ARG cc_start: 0.7731 (tpm170) cc_final: 0.7339 (tpm170) REVERT: H 540 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.5480 (mp10) REVERT: I 4 LEU cc_start: 0.8733 (mt) cc_final: 0.8411 (mp) REVERT: I 82 SER cc_start: 0.8045 (m) cc_final: 0.7615 (t) REVERT: J 45 ARG cc_start: 0.7916 (ptt180) cc_final: 0.7609 (ttp-170) REVERT: J 54 ARG cc_start: 0.7683 (mtt90) cc_final: 0.7277 (mtm-85) REVERT: J 77 ASN cc_start: 0.7705 (t0) cc_final: 0.6882 (t0) REVERT: J 79 GLU cc_start: 0.4923 (mp0) cc_final: 0.4615 (mp0) REVERT: K 31 ARG cc_start: 0.6630 (ptm-80) cc_final: 0.6405 (ptm-80) REVERT: K 87 TYR cc_start: 0.6340 (m-80) cc_final: 0.6098 (m-80) REVERT: L 36 TRP cc_start: 0.6554 (m100) cc_final: 0.5699 (m100) REVERT: L 99 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7677 (ttm170) REVERT: L 100 MET cc_start: 0.6019 (mtt) cc_final: 0.5686 (mpp) REVERT: O 92 ASN cc_start: 0.8193 (m-40) cc_final: 0.7156 (t0) REVERT: O 195 ASN cc_start: 0.7014 (m-40) cc_final: 0.6806 (m-40) REVERT: P 519 PHE cc_start: 0.7571 (t80) cc_final: 0.7172 (t80) outliers start: 78 outliers final: 48 residues processed: 445 average time/residue: 0.1969 time to fit residues: 134.9058 Evaluate side-chains 407 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 356 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 47 ILE Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 584 GLU Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 637 ASN Chi-restraints excluded: chain P residue 652 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 261 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 232 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 205 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 34 GLN Q 50 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN ** H 540 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 = 0.4131 r_free = 0.4131 target = 0.168821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125959 restraints weight = 38986.874| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 3.77 r_work: 0.3338 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27183 Z= 0.134 Angle : 0.610 11.827 37215 Z= 0.289 Chirality : 0.045 0.470 4515 Planarity : 0.004 0.034 4464 Dihedral : 8.099 77.389 6537 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.00 % Allowed : 10.14 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.15), residues: 3048 helix: 1.36 (0.25), residues: 438 sheet: 1.02 (0.16), residues: 933 loop : 1.12 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 31 TYR 0.018 0.001 TYR E 36 PHE 0.013 0.001 PHE O 317 TRP 0.027 0.002 TRP R 36 HIS 0.004 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00306 (26979) covalent geometry : angle 0.56482 (36651) SS BOND : bond 0.00459 ( 48) SS BOND : angle 1.50851 ( 96) hydrogen bonds : bond 0.04119 ( 767) hydrogen bonds : angle 5.48233 ( 1935) link_ALPHA1-2 : bond 0.00735 ( 9) link_ALPHA1-2 : angle 1.69990 ( 27) link_ALPHA1-3 : bond 0.00946 ( 12) link_ALPHA1-3 : angle 1.32413 ( 36) link_ALPHA1-6 : bond 0.00489 ( 15) link_ALPHA1-6 : angle 1.71783 ( 45) link_BETA1-4 : bond 0.00518 ( 57) link_BETA1-4 : angle 1.99427 ( 171) link_NAG-ASN : bond 0.00260 ( 63) link_NAG-ASN : angle 2.26925 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 374 time to evaluate : 1.002 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: M 69 MET cc_start: 0.8627 (mtt) cc_final: 0.8039 (mtt) REVERT: M 72 ASP cc_start: 0.8456 (t70) cc_final: 0.8237 (t70) REVERT: M 82 SER cc_start: 0.8162 (m) cc_final: 0.7742 (t) REVERT: N 77 ASN cc_start: 0.7836 (t0) cc_final: 0.7214 (t0) REVERT: Q 31 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.5601 (ptp-170) REVERT: Q 35 TRP cc_start: 0.7827 (m100) cc_final: 0.7447 (m100) REVERT: R 34 TRP cc_start: 0.5575 (m100) cc_final: 0.5349 (m100) REVERT: R 100 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: R 100 MET cc_start: 0.8089 (mpp) cc_final: 0.7308 (mpp) REVERT: A 92 ASN cc_start: 0.8008 (m-40) cc_final: 0.7233 (t0) REVERT: A 252 ARG cc_start: 0.8394 (mtt90) cc_final: 0.7908 (mtt-85) REVERT: B 588 ARG cc_start: 0.8111 (tpt170) cc_final: 0.7225 (ttm170) REVERT: C 82 SER cc_start: 0.8144 (m) cc_final: 0.7731 (t) REVERT: D 45 ARG cc_start: 0.8011 (ptt180) cc_final: 0.7124 (ptp90) REVERT: D 77 ASN cc_start: 0.7562 (t0) cc_final: 0.6880 (t0) REVERT: D 79 GLU cc_start: 0.4599 (mp0) cc_final: 0.4231 (mp0) REVERT: E 31 ARG cc_start: 0.6806 (ptm-80) cc_final: 0.6506 (ptm-80) REVERT: E 89 HIS cc_start: 0.5008 (t-170) cc_final: 0.4707 (t-170) REVERT: F 36 TRP cc_start: 0.6504 (m100) cc_final: 0.6034 (m100) REVERT: F 47 TRP cc_start: 0.6384 (t60) cc_final: 0.5811 (t-100) REVERT: F 90 TYR cc_start: 0.6668 (m-10) cc_final: 0.6367 (m-10) REVERT: F 97 HIS cc_start: 0.6801 (p90) cc_final: 0.6553 (p90) REVERT: F 100 PHE cc_start: 0.5466 (t80) cc_final: 0.4964 (t80) REVERT: F 100 MET cc_start: 0.7746 (mpp) cc_final: 0.6429 (mtt) REVERT: G 92 ASN cc_start: 0.8026 (m-40) cc_final: 0.7071 (t0) REVERT: G 504 ARG cc_start: 0.7729 (tpm170) cc_final: 0.7339 (tpm170) REVERT: H 540 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.5658 (mp10) REVERT: I 4 LEU cc_start: 0.8741 (mt) cc_final: 0.8500 (mp) REVERT: I 32 CYS cc_start: 0.7118 (m) cc_final: 0.6813 (m) REVERT: I 82 SER cc_start: 0.8084 (m) cc_final: 0.7650 (t) REVERT: J 45 ARG cc_start: 0.7915 (ptt180) cc_final: 0.7588 (ttp-170) REVERT: J 54 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7459 (mtt90) REVERT: J 77 ASN cc_start: 0.7730 (t0) cc_final: 0.6887 (t0) REVERT: J 79 GLU cc_start: 0.4835 (mp0) cc_final: 0.4443 (mp0) REVERT: L 97 HIS cc_start: 0.7176 (p90) cc_final: 0.6685 (p-80) REVERT: L 99 ARG cc_start: 0.8100 (ttm170) cc_final: 0.7555 (ttm170) REVERT: L 100 MET cc_start: 0.6237 (mtt) cc_final: 0.5701 (mpp) REVERT: O 92 ASN cc_start: 0.8225 (m-40) cc_final: 0.7261 (t0) REVERT: O 99 ASN cc_start: 0.7911 (t0) cc_final: 0.7480 (m-40) REVERT: P 519 PHE cc_start: 0.7734 (t80) cc_final: 0.7325 (t80) outliers start: 81 outliers final: 60 residues processed: 426 average time/residue: 0.1923 time to fit residues: 126.6495 Evaluate side-chains 411 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 348 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 31 ARG Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 100 GLU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 70 ASP Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 584 GLU Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 616 ASN Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 22 SER Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 196 CYS Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain P residue 637 ASN Chi-restraints excluded: chain P residue 652 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 135 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 100 GLN R 97 HIS ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS D 37 GLN F 97 HIS G 442 GLN ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 374 HIS P 658 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111178 restraints weight = 38533.567| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.21 r_work: 0.3208 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 27183 Z= 0.322 Angle : 0.768 10.466 37215 Z= 0.372 Chirality : 0.049 0.266 4515 Planarity : 0.005 0.089 4464 Dihedral : 8.547 79.818 6537 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.14 % Allowed : 10.32 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3048 helix: 0.47 (0.24), residues: 438 sheet: 0.36 (0.16), residues: 951 loop : 0.45 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 39 TYR 0.027 0.002 TYR M 59 PHE 0.020 0.003 PHE M 100D TRP 0.039 0.003 TRP L 36 HIS 0.007 0.002 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00773 (26979) covalent geometry : angle 0.72468 (36651) SS BOND : bond 0.00772 ( 48) SS BOND : angle 1.79404 ( 96) hydrogen bonds : bond 0.04983 ( 767) hydrogen bonds : angle 5.88984 ( 1935) link_ALPHA1-2 : bond 0.00644 ( 9) link_ALPHA1-2 : angle 1.75676 ( 27) link_ALPHA1-3 : bond 0.00677 ( 12) link_ALPHA1-3 : angle 1.42356 ( 36) link_ALPHA1-6 : bond 0.00474 ( 15) link_ALPHA1-6 : angle 1.92793 ( 45) link_BETA1-4 : bond 0.00458 ( 57) link_BETA1-4 : angle 2.17386 ( 171) link_NAG-ASN : bond 0.00545 ( 63) link_NAG-ASN : angle 2.59178 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 369 time to evaluate : 0.861 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: M 72 ASP cc_start: 0.8531 (t70) cc_final: 0.8317 (t70) REVERT: M 82 SER cc_start: 0.8199 (m) cc_final: 0.7801 (t) REVERT: M 105 ARG cc_start: 0.8199 (mmt180) cc_final: 0.7754 (mmt180) REVERT: N 52 SER cc_start: 0.7241 (p) cc_final: 0.6969 (t) REVERT: N 77 ASN cc_start: 0.7796 (t0) cc_final: 0.7144 (t0) REVERT: Q 73 LEU cc_start: 0.6274 (tp) cc_final: 0.6018 (tp) REVERT: R 34 TRP cc_start: 0.5458 (m100) cc_final: 0.5152 (m100) REVERT: R 100 MET cc_start: 0.8263 (mpp) cc_final: 0.7149 (mpp) REVERT: A 92 ASN cc_start: 0.8001 (m-40) cc_final: 0.6977 (t0) REVERT: A 432 LYS cc_start: 0.8693 (mttm) cc_final: 0.8303 (mtmm) REVERT: B 626 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6571 (ttm) REVERT: B 634 GLU cc_start: 0.7742 (tt0) cc_final: 0.7503 (tt0) REVERT: C 82 SER cc_start: 0.8129 (m) cc_final: 0.7697 (t) REVERT: D 45 ARG cc_start: 0.8021 (ptt180) cc_final: 0.7166 (ptp90) REVERT: D 77 ASN cc_start: 0.7723 (t0) cc_final: 0.7169 (t0) REVERT: E 31 ARG cc_start: 0.6832 (ptm-80) cc_final: 0.6555 (ptm-80) REVERT: E 87 TYR cc_start: 0.6274 (m-80) cc_final: 0.6001 (m-80) REVERT: F 47 TRP cc_start: 0.6422 (t60) cc_final: 0.5766 (t-100) REVERT: F 100 PHE cc_start: 0.5418 (t80) cc_final: 0.4843 (t80) REVERT: F 100 MET cc_start: 0.7960 (mpp) cc_final: 0.6632 (mtt) REVERT: H 519 PHE cc_start: 0.7981 (t80) cc_final: 0.7523 (t80) REVERT: H 540 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.5526 (mp10) REVERT: H 546 SER cc_start: 0.7789 (t) cc_final: 0.7536 (p) REVERT: I 82 SER cc_start: 0.8165 (m) cc_final: 0.7745 (t) REVERT: J 54 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7592 (mtm-85) REVERT: J 77 ASN cc_start: 0.7840 (t0) cc_final: 0.7385 (t0) REVERT: J 82 ASP cc_start: 0.4816 (m-30) cc_final: 0.4580 (t0) REVERT: L 97 HIS cc_start: 0.7579 (p90) cc_final: 0.7229 (p-80) REVERT: O 92 ASN cc_start: 0.8188 (m-40) cc_final: 0.7144 (t0) REVERT: O 99 ASN cc_start: 0.8189 (t0) cc_final: 0.7791 (m-40) REVERT: O 426 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6655 (mmt) REVERT: P 626 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6937 (ttm) outliers start: 112 outliers final: 89 residues processed: 441 average time/residue: 0.1895 time to fit residues: 130.7021 Evaluate side-chains 430 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 337 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 543 ASN Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 616 ASN Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain H residue 644 THR Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 75 SER Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 194 ILE Chi-restraints excluded: chain O residue 196 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain O residue 426 MET Chi-restraints excluded: chain O residue 430 VAL Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain P residue 626 MET Chi-restraints excluded: chain P residue 637 ASN Chi-restraints excluded: chain P residue 644 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 221 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 264 optimal weight: 0.9980 chunk 229 optimal weight: 10.0000 chunk 225 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN E 50 ASN F 97 HIS G 103 GLN G 280 ASN ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 ASN P 577 GLN P 616 ASN P 658 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.165115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.122001 restraints weight = 39032.184| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 3.82 r_work: 0.3274 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27183 Z= 0.144 Angle : 0.605 10.144 37215 Z= 0.291 Chirality : 0.044 0.248 4515 Planarity : 0.004 0.051 4464 Dihedral : 7.994 77.656 6537 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.14 % Allowed : 12.17 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3048 helix: 0.88 (0.24), residues: 438 sheet: 0.32 (0.16), residues: 975 loop : 0.47 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 61 TYR 0.015 0.001 TYR Q 49 PHE 0.012 0.001 PHE N 98 TRP 0.035 0.002 TRP K 35 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00334 (26979) covalent geometry : angle 0.56457 (36651) SS BOND : bond 0.00392 ( 48) SS BOND : angle 1.50149 ( 96) hydrogen bonds : bond 0.04026 ( 767) hydrogen bonds : angle 5.57280 ( 1935) link_ALPHA1-2 : bond 0.00650 ( 9) link_ALPHA1-2 : angle 1.65959 ( 27) link_ALPHA1-3 : bond 0.00926 ( 12) link_ALPHA1-3 : angle 1.36054 ( 36) link_ALPHA1-6 : bond 0.00544 ( 15) link_ALPHA1-6 : angle 1.73695 ( 45) link_BETA1-4 : bond 0.00408 ( 57) link_BETA1-4 : angle 1.84704 ( 171) link_NAG-ASN : bond 0.00236 ( 63) link_NAG-ASN : angle 2.13427 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 355 time to evaluate : 1.069 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: M 69 MET cc_start: 0.8719 (mtt) cc_final: 0.8203 (mtt) REVERT: M 72 ASP cc_start: 0.8397 (t70) cc_final: 0.8191 (t70) REVERT: M 82 SER cc_start: 0.8095 (m) cc_final: 0.7693 (t) REVERT: N 77 ASN cc_start: 0.7811 (t0) cc_final: 0.7235 (t0) REVERT: R 33 TYR cc_start: 0.6888 (m-80) cc_final: 0.6378 (m-80) REVERT: R 97 HIS cc_start: 0.7158 (p-80) cc_final: 0.6455 (p-80) REVERT: R 100 ASN cc_start: 0.8108 (m-40) cc_final: 0.7874 (m-40) REVERT: R 100 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: R 100 MET cc_start: 0.8193 (mpp) cc_final: 0.6651 (mpp) REVERT: A 82 GLN cc_start: 0.6775 (mp10) cc_final: 0.6523 (mp10) REVERT: A 92 ASN cc_start: 0.8014 (m-40) cc_final: 0.7180 (t0) REVERT: A 432 LYS cc_start: 0.8665 (mttm) cc_final: 0.8262 (mtmm) REVERT: B 626 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6560 (ttm) REVERT: C 48 MET cc_start: 0.8669 (mtt) cc_final: 0.8447 (ttm) REVERT: C 82 SER cc_start: 0.8037 (m) cc_final: 0.7593 (t) REVERT: C 87 THR cc_start: 0.8938 (m) cc_final: 0.8529 (p) REVERT: D 45 ARG cc_start: 0.8003 (ptt180) cc_final: 0.7124 (ptp90) REVERT: D 77 ASN cc_start: 0.7671 (t0) cc_final: 0.7070 (t0) REVERT: D 79 GLU cc_start: 0.5379 (mp0) cc_final: 0.4967 (mp0) REVERT: D 82 ASP cc_start: 0.6079 (m-30) cc_final: 0.5014 (t0) REVERT: E 31 ARG cc_start: 0.6804 (ptm-80) cc_final: 0.6529 (ptm-80) REVERT: E 87 TYR cc_start: 0.6244 (m-80) cc_final: 0.5873 (m-80) REVERT: F 36 TRP cc_start: 0.6772 (m100) cc_final: 0.6187 (m100) REVERT: F 47 TRP cc_start: 0.6517 (t60) cc_final: 0.5328 (t-100) REVERT: F 100 PHE cc_start: 0.5392 (t80) cc_final: 0.4863 (t80) REVERT: F 100 MET cc_start: 0.8109 (mpp) cc_final: 0.7474 (mpp) REVERT: G 92 ASN cc_start: 0.8080 (m-40) cc_final: 0.7090 (t0) REVERT: G 205 CYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6465 (m) REVERT: H 519 PHE cc_start: 0.7878 (t80) cc_final: 0.7483 (t80) REVERT: H 520 LEU cc_start: 0.7764 (mm) cc_final: 0.6934 (pp) REVERT: H 540 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.5434 (mp10) REVERT: H 546 SER cc_start: 0.7820 (t) cc_final: 0.7597 (p) REVERT: I 82 SER cc_start: 0.8119 (m) cc_final: 0.7688 (t) REVERT: J 54 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7586 (mtm-85) REVERT: J 77 ASN cc_start: 0.7925 (t0) cc_final: 0.6948 (t0) REVERT: K 70 THR cc_start: 0.7848 (p) cc_final: 0.7636 (p) REVERT: K 87 TYR cc_start: 0.6884 (m-80) cc_final: 0.6263 (m-80) REVERT: L 97 HIS cc_start: 0.7578 (p90) cc_final: 0.7240 (p-80) REVERT: O 92 ASN cc_start: 0.8234 (m-40) cc_final: 0.7239 (t0) REVERT: O 99 ASN cc_start: 0.8241 (t0) cc_final: 0.7671 (m-40) REVERT: O 205 CYS cc_start: 0.6653 (OUTLIER) cc_final: 0.6261 (m) REVERT: O 426 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6444 (mmt) REVERT: P 626 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6947 (ttm) outliers start: 85 outliers final: 57 residues processed: 405 average time/residue: 0.1927 time to fit residues: 121.1825 Evaluate side-chains 396 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 332 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 100 GLU Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 616 ASN Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 196 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain O residue 426 MET Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 626 MET Chi-restraints excluded: chain P residue 637 ASN Chi-restraints excluded: chain P residue 652 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 107 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 120 optimal weight: 0.6980 chunk 236 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN E 50 ASN F 97 HIS ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 100HASN P 616 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.159763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107835 restraints weight = 39540.272| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.17 r_work: 0.3209 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 27183 Z= 0.340 Angle : 0.782 9.564 37215 Z= 0.379 Chirality : 0.050 0.256 4515 Planarity : 0.005 0.059 4464 Dihedral : 8.447 79.741 6537 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.63 % Allowed : 11.91 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 3048 helix: 0.45 (0.25), residues: 420 sheet: -0.18 (0.16), residues: 999 loop : 0.05 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 23 TYR 0.027 0.003 TYR O 486 PHE 0.020 0.003 PHE C 100D TRP 0.025 0.003 TRP R 36 HIS 0.007 0.002 HIS K 89 Details of bonding type rmsd covalent geometry : bond 0.00823 (26979) covalent geometry : angle 0.74042 (36651) SS BOND : bond 0.00649 ( 48) SS BOND : angle 1.99937 ( 96) hydrogen bonds : bond 0.04956 ( 767) hydrogen bonds : angle 5.94426 ( 1935) link_ALPHA1-2 : bond 0.00682 ( 9) link_ALPHA1-2 : angle 1.71305 ( 27) link_ALPHA1-3 : bond 0.00738 ( 12) link_ALPHA1-3 : angle 1.47574 ( 36) link_ALPHA1-6 : bond 0.00524 ( 15) link_ALPHA1-6 : angle 1.93398 ( 45) link_BETA1-4 : bond 0.00448 ( 57) link_BETA1-4 : angle 2.11910 ( 171) link_NAG-ASN : bond 0.00577 ( 63) link_NAG-ASN : angle 2.52877 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 347 time to evaluate : 1.059 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: M 72 ASP cc_start: 0.8444 (t70) cc_final: 0.8237 (t70) REVERT: M 82 SER cc_start: 0.8083 (m) cc_final: 0.7781 (t) REVERT: N 52 SER cc_start: 0.7194 (p) cc_final: 0.6925 (t) REVERT: N 77 ASN cc_start: 0.7807 (t0) cc_final: 0.7309 (t0) REVERT: N 82 ASP cc_start: 0.6429 (m-30) cc_final: 0.5006 (t0) REVERT: R 100 ASN cc_start: 0.8208 (m-40) cc_final: 0.7983 (m-40) REVERT: A 411 ASN cc_start: 0.5523 (t0) cc_final: 0.4087 (p0) REVERT: A 432 LYS cc_start: 0.8642 (mttm) cc_final: 0.8297 (mtmm) REVERT: C 82 SER cc_start: 0.8008 (m) cc_final: 0.7540 (t) REVERT: C 87 THR cc_start: 0.8883 (m) cc_final: 0.8450 (p) REVERT: D 37 GLN cc_start: 0.7617 (tt0) cc_final: 0.7324 (tt0) REVERT: D 45 ARG cc_start: 0.8033 (ptt180) cc_final: 0.7287 (ptp90) REVERT: D 77 ASN cc_start: 0.7719 (t0) cc_final: 0.7185 (t0) REVERT: D 82 ASP cc_start: 0.6145 (m-30) cc_final: 0.5126 (t0) REVERT: E 31 ARG cc_start: 0.7030 (ptm-80) cc_final: 0.6769 (ptm-80) REVERT: E 50 ASN cc_start: 0.5486 (t0) cc_final: 0.4677 (t0) REVERT: E 87 TYR cc_start: 0.6482 (m-80) cc_final: 0.6171 (m-80) REVERT: F 36 TRP cc_start: 0.6959 (m100) cc_final: 0.6276 (m100) REVERT: F 47 TRP cc_start: 0.6516 (t60) cc_final: 0.5383 (t-100) REVERT: F 100 PHE cc_start: 0.5741 (t80) cc_final: 0.5166 (t80) REVERT: F 100 THR cc_start: 0.8608 (p) cc_final: 0.8323 (p) REVERT: G 114 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: H 519 PHE cc_start: 0.8036 (t80) cc_final: 0.7643 (t80) REVERT: H 520 LEU cc_start: 0.7774 (mm) cc_final: 0.6959 (pp) REVERT: H 540 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.5530 (mp10) REVERT: H 626 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.6980 (ttm) REVERT: I 82 SER cc_start: 0.8061 (m) cc_final: 0.7649 (t) REVERT: J 77 ASN cc_start: 0.7545 (t0) cc_final: 0.6910 (t0) REVERT: K 70 THR cc_start: 0.8071 (p) cc_final: 0.7661 (p) REVERT: K 87 TYR cc_start: 0.6836 (m-80) cc_final: 0.6593 (m-80) REVERT: L 97 HIS cc_start: 0.7720 (p90) cc_final: 0.7350 (p-80) REVERT: O 92 ASN cc_start: 0.8156 (m-40) cc_final: 0.7181 (t0) REVERT: O 99 ASN cc_start: 0.8485 (t0) cc_final: 0.7982 (m-40) REVERT: O 426 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6596 (mmt) outliers start: 98 outliers final: 75 residues processed: 411 average time/residue: 0.1817 time to fit residues: 116.8317 Evaluate side-chains 412 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 333 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 543 ASN Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 616 ASN Chi-restraints excluded: chain H residue 626 MET Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain H residue 644 THR Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 196 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain O residue 426 MET Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain P residue 637 ASN Chi-restraints excluded: chain P residue 652 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 294 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 1 GLN R 58 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100HASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.164380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117340 restraints weight = 39537.192| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.65 r_work: 0.3281 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27183 Z= 0.135 Angle : 0.597 9.697 37215 Z= 0.289 Chirality : 0.044 0.232 4515 Planarity : 0.004 0.044 4464 Dihedral : 7.654 76.956 6537 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.44 % Allowed : 13.39 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 3048 helix: 1.07 (0.25), residues: 420 sheet: -0.01 (0.16), residues: 999 loop : 0.27 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 23 TYR 0.018 0.001 TYR A 173 PHE 0.010 0.001 PHE N 98 TRP 0.025 0.002 TRP R 36 HIS 0.004 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00314 (26979) covalent geometry : angle 0.55817 (36651) SS BOND : bond 0.00483 ( 48) SS BOND : angle 1.65617 ( 96) hydrogen bonds : bond 0.03829 ( 767) hydrogen bonds : angle 5.53843 ( 1935) link_ALPHA1-2 : bond 0.00694 ( 9) link_ALPHA1-2 : angle 1.53342 ( 27) link_ALPHA1-3 : bond 0.00962 ( 12) link_ALPHA1-3 : angle 1.36538 ( 36) link_ALPHA1-6 : bond 0.00565 ( 15) link_ALPHA1-6 : angle 1.67252 ( 45) link_BETA1-4 : bond 0.00426 ( 57) link_BETA1-4 : angle 1.78113 ( 171) link_NAG-ASN : bond 0.00222 ( 63) link_NAG-ASN : angle 2.00793 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 348 time to evaluate : 0.767 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: M 82 SER cc_start: 0.8050 (m) cc_final: 0.7714 (t) REVERT: N 52 SER cc_start: 0.7287 (p) cc_final: 0.7051 (t) REVERT: N 77 ASN cc_start: 0.7841 (t0) cc_final: 0.7362 (t0) REVERT: N 82 ASP cc_start: 0.6176 (m-30) cc_final: 0.5118 (t0) REVERT: R 100 MET cc_start: 0.8155 (mpp) cc_final: 0.6634 (mpp) REVERT: A 92 ASN cc_start: 0.8007 (m-40) cc_final: 0.7074 (t0) REVERT: A 252 ARG cc_start: 0.8393 (mtt90) cc_final: 0.8079 (mtt-85) REVERT: A 432 LYS cc_start: 0.8664 (mttm) cc_final: 0.8411 (mttp) REVERT: B 626 MET cc_start: 0.7812 (ttt) cc_final: 0.7012 (ttm) REVERT: C 82 SER cc_start: 0.7909 (m) cc_final: 0.7450 (t) REVERT: C 87 THR cc_start: 0.8910 (m) cc_final: 0.8487 (p) REVERT: D 45 ARG cc_start: 0.7927 (ptt180) cc_final: 0.7172 (ptp90) REVERT: D 77 ASN cc_start: 0.7552 (t0) cc_final: 0.6894 (t0) REVERT: D 79 GLU cc_start: 0.5259 (mp0) cc_final: 0.4963 (mp0) REVERT: D 82 ASP cc_start: 0.5814 (m-30) cc_final: 0.4951 (t0) REVERT: E 87 TYR cc_start: 0.6292 (m-80) cc_final: 0.5960 (m-80) REVERT: F 36 TRP cc_start: 0.6723 (m100) cc_final: 0.6166 (m100) REVERT: F 47 TRP cc_start: 0.6371 (t60) cc_final: 0.5144 (t-100) REVERT: F 90 TYR cc_start: 0.6710 (m-10) cc_final: 0.6494 (m-10) REVERT: F 97 HIS cc_start: 0.7396 (p-80) cc_final: 0.6976 (p90) REVERT: F 100 PHE cc_start: 0.5540 (t80) cc_final: 0.5010 (t80) REVERT: F 100 THR cc_start: 0.8503 (p) cc_final: 0.8192 (p) REVERT: G 92 ASN cc_start: 0.8066 (m-40) cc_final: 0.7119 (t0) REVERT: H 520 LEU cc_start: 0.7716 (mm) cc_final: 0.6895 (pp) REVERT: H 540 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.5422 (mp10) REVERT: I 72 ASP cc_start: 0.8349 (t0) cc_final: 0.7998 (t70) REVERT: I 82 SER cc_start: 0.8018 (m) cc_final: 0.7553 (t) REVERT: J 5 THR cc_start: 0.8162 (m) cc_final: 0.7800 (p) REVERT: J 77 ASN cc_start: 0.7557 (t0) cc_final: 0.6832 (t0) REVERT: K 70 THR cc_start: 0.7992 (OUTLIER) cc_final: 0.7672 (p) REVERT: K 87 TYR cc_start: 0.6717 (m-80) cc_final: 0.6450 (m-80) REVERT: L 97 HIS cc_start: 0.7678 (p90) cc_final: 0.7290 (p-80) REVERT: L 100 PHE cc_start: 0.5316 (t80) cc_final: 0.4760 (t80) REVERT: O 92 ASN cc_start: 0.8208 (m-40) cc_final: 0.7208 (t0) REVERT: O 99 ASN cc_start: 0.8324 (t0) cc_final: 0.7808 (m-40) REVERT: O 426 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6322 (mmt) REVERT: O 463 ASN cc_start: 0.7543 (m-40) cc_final: 0.7296 (p0) outliers start: 66 outliers final: 48 residues processed: 387 average time/residue: 0.1860 time to fit residues: 111.6602 Evaluate side-chains 386 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 335 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 616 ASN Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 196 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain O residue 426 MET Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 637 ASN Chi-restraints excluded: chain P residue 652 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 276 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN ** H 540 GLN ** 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 = 0.4052 r_free = 0.4052 target = 0.160593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112777 restraints weight = 39691.564| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.60 r_work: 0.3212 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 27183 Z= 0.285 Angle : 0.717 9.303 37215 Z= 0.347 Chirality : 0.047 0.241 4515 Planarity : 0.005 0.046 4464 Dihedral : 7.931 78.696 6537 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.96 % Allowed : 12.91 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3048 helix: 0.40 (0.24), residues: 453 sheet: -0.12 (0.16), residues: 951 loop : -0.10 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 61 TYR 0.018 0.002 TYR O 486 PHE 0.018 0.002 PHE J 98 TRP 0.031 0.002 TRP R 36 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00688 (26979) covalent geometry : angle 0.67764 (36651) SS BOND : bond 0.00508 ( 48) SS BOND : angle 1.89544 ( 96) hydrogen bonds : bond 0.04538 ( 767) hydrogen bonds : angle 5.78604 ( 1935) link_ALPHA1-2 : bond 0.00673 ( 9) link_ALPHA1-2 : angle 1.60069 ( 27) link_ALPHA1-3 : bond 0.00734 ( 12) link_ALPHA1-3 : angle 1.47142 ( 36) link_ALPHA1-6 : bond 0.00531 ( 15) link_ALPHA1-6 : angle 1.80128 ( 45) link_BETA1-4 : bond 0.00420 ( 57) link_BETA1-4 : angle 1.97272 ( 171) link_NAG-ASN : bond 0.00482 ( 63) link_NAG-ASN : angle 2.29680 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 336 time to evaluate : 0.814 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: M 82 SER cc_start: 0.8044 (m) cc_final: 0.7709 (t) REVERT: N 52 SER cc_start: 0.7212 (p) cc_final: 0.6980 (t) REVERT: N 77 ASN cc_start: 0.7832 (t0) cc_final: 0.7177 (t0) REVERT: N 82 ASP cc_start: 0.6209 (m-30) cc_final: 0.5099 (t0) REVERT: Q 35 TRP cc_start: 0.7636 (m100) cc_final: 0.7325 (m100) REVERT: R 100 ASN cc_start: 0.8192 (m-40) cc_final: 0.7965 (m-40) REVERT: R 100 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.7259 (p90) REVERT: R 100 MET cc_start: 0.8277 (mpp) cc_final: 0.6417 (mpp) REVERT: A 92 ASN cc_start: 0.7981 (m-40) cc_final: 0.6981 (t0) REVERT: A 432 LYS cc_start: 0.8646 (mttm) cc_final: 0.8395 (mttp) REVERT: C 82 SER cc_start: 0.7970 (m) cc_final: 0.7515 (t) REVERT: C 87 THR cc_start: 0.8914 (m) cc_final: 0.8474 (p) REVERT: C 105 ARG cc_start: 0.8240 (mmt180) cc_final: 0.7987 (mmt180) REVERT: D 37 GLN cc_start: 0.7580 (tt0) cc_final: 0.7254 (tt0) REVERT: D 45 ARG cc_start: 0.7966 (ptt180) cc_final: 0.7156 (ptp90) REVERT: D 77 ASN cc_start: 0.7624 (t0) cc_final: 0.6930 (t0) REVERT: D 79 GLU cc_start: 0.5368 (mp0) cc_final: 0.5023 (mp0) REVERT: D 82 ASP cc_start: 0.6006 (m-30) cc_final: 0.5521 (t70) REVERT: E 87 TYR cc_start: 0.6363 (m-80) cc_final: 0.6036 (m-80) REVERT: F 36 TRP cc_start: 0.6850 (m100) cc_final: 0.6177 (m100) REVERT: F 47 TRP cc_start: 0.6475 (t60) cc_final: 0.5246 (t-100) REVERT: F 97 HIS cc_start: 0.7469 (p-80) cc_final: 0.6956 (p90) REVERT: F 100 PHE cc_start: 0.5648 (t80) cc_final: 0.5102 (t80) REVERT: F 100 THR cc_start: 0.8563 (p) cc_final: 0.8251 (p) REVERT: G 92 ASN cc_start: 0.8089 (m-40) cc_final: 0.7131 (t0) REVERT: G 114 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: H 520 LEU cc_start: 0.7601 (mm) cc_final: 0.6930 (pp) REVERT: H 540 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.5536 (mp10) REVERT: I 82 SER cc_start: 0.8010 (m) cc_final: 0.7558 (t) REVERT: J 5 THR cc_start: 0.8257 (m) cc_final: 0.7875 (p) REVERT: J 77 ASN cc_start: 0.7492 (t0) cc_final: 0.6748 (t0) REVERT: K 70 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7761 (p) REVERT: K 87 TYR cc_start: 0.6728 (m-80) cc_final: 0.6436 (m-80) REVERT: L 97 HIS cc_start: 0.7721 (p90) cc_final: 0.7328 (p-80) REVERT: O 92 ASN cc_start: 0.8178 (m-40) cc_final: 0.7200 (t0) REVERT: O 99 ASN cc_start: 0.8415 (t0) cc_final: 0.7872 (m-40) REVERT: O 426 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6509 (mmt) outliers start: 80 outliers final: 66 residues processed: 390 average time/residue: 0.1728 time to fit residues: 105.1663 Evaluate side-chains 406 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 335 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 17 SER Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 584 GLU Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 616 ASN Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain H residue 644 THR Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 196 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 245 VAL Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain O residue 426 MET Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 544 LEU Chi-restraints excluded: chain P residue 637 ASN Chi-restraints excluded: chain P residue 652 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 58 optimal weight: 0.0040 chunk 100 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 144 optimal weight: 0.0000 chunk 37 optimal weight: 5.9990 chunk 213 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 246 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 1 GLN ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.163922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122461 restraints weight = 39101.520| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.47 r_work: 0.3299 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27183 Z= 0.119 Angle : 0.578 9.208 37215 Z= 0.280 Chirality : 0.043 0.218 4515 Planarity : 0.004 0.040 4464 Dihedral : 7.228 76.137 6537 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.11 % Allowed : 13.98 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3048 helix: 0.97 (0.24), residues: 453 sheet: 0.11 (0.17), residues: 930 loop : 0.11 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 61 TYR 0.018 0.001 TYR J 49 PHE 0.011 0.001 PHE M 29 TRP 0.035 0.002 TRP R 36 HIS 0.004 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00274 (26979) covalent geometry : angle 0.54264 (36651) SS BOND : bond 0.00373 ( 48) SS BOND : angle 1.62941 ( 96) hydrogen bonds : bond 0.03544 ( 767) hydrogen bonds : angle 5.40001 ( 1935) link_ALPHA1-2 : bond 0.00612 ( 9) link_ALPHA1-2 : angle 1.49831 ( 27) link_ALPHA1-3 : bond 0.00950 ( 12) link_ALPHA1-3 : angle 1.36414 ( 36) link_ALPHA1-6 : bond 0.00579 ( 15) link_ALPHA1-6 : angle 1.59552 ( 45) link_BETA1-4 : bond 0.00434 ( 57) link_BETA1-4 : angle 1.68902 ( 171) link_NAG-ASN : bond 0.00197 ( 63) link_NAG-ASN : angle 1.86149 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 357 time to evaluate : 0.950 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: M 82 SER cc_start: 0.8037 (m) cc_final: 0.7691 (t) REVERT: N 5 THR cc_start: 0.8449 (m) cc_final: 0.8096 (p) REVERT: N 77 ASN cc_start: 0.7721 (t0) cc_final: 0.7127 (t0) REVERT: N 82 ASP cc_start: 0.6012 (m-30) cc_final: 0.5128 (t0) REVERT: R 100 ASN cc_start: 0.8144 (m-40) cc_final: 0.7935 (m-40) REVERT: R 100 MET cc_start: 0.8263 (mpp) cc_final: 0.6430 (mpp) REVERT: A 92 ASN cc_start: 0.7984 (m-40) cc_final: 0.7217 (t0) REVERT: A 252 ARG cc_start: 0.8373 (mtt90) cc_final: 0.8083 (mtt-85) REVERT: A 432 LYS cc_start: 0.8641 (mttm) cc_final: 0.8380 (mttp) REVERT: B 626 MET cc_start: 0.7815 (ttt) cc_final: 0.6968 (ttm) REVERT: C 82 SER cc_start: 0.7892 (m) cc_final: 0.7436 (t) REVERT: D 45 ARG cc_start: 0.7888 (ptt180) cc_final: 0.7146 (ptp90) REVERT: D 77 ASN cc_start: 0.7568 (t0) cc_final: 0.6911 (t0) REVERT: D 82 ASP cc_start: 0.5687 (m-30) cc_final: 0.4948 (t0) REVERT: E 87 TYR cc_start: 0.6229 (m-80) cc_final: 0.5920 (m-80) REVERT: F 47 TRP cc_start: 0.6389 (t60) cc_final: 0.5116 (t-100) REVERT: F 97 HIS cc_start: 0.7565 (p-80) cc_final: 0.7027 (p90) REVERT: F 100 PHE cc_start: 0.5478 (t80) cc_final: 0.4985 (t80) REVERT: G 92 ASN cc_start: 0.8054 (m-40) cc_final: 0.7153 (t0) REVERT: G 114 GLN cc_start: 0.8140 (mt0) cc_final: 0.7868 (mt0) REVERT: H 520 LEU cc_start: 0.7561 (mm) cc_final: 0.6893 (pp) REVERT: H 540 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.5457 (mp10) REVERT: I 72 ASP cc_start: 0.8327 (t0) cc_final: 0.8000 (t70) REVERT: I 82 SER cc_start: 0.7969 (m) cc_final: 0.7500 (t) REVERT: J 5 THR cc_start: 0.8255 (m) cc_final: 0.7921 (p) REVERT: K 70 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7718 (p) REVERT: K 87 TYR cc_start: 0.6632 (m-80) cc_final: 0.6317 (m-80) REVERT: L 100 PHE cc_start: 0.5366 (t80) cc_final: 0.4804 (t80) REVERT: O 66 ARG cc_start: 0.7893 (mtp180) cc_final: 0.7546 (ttp-170) REVERT: O 92 ASN cc_start: 0.8168 (m-40) cc_final: 0.7231 (t0) REVERT: O 99 ASN cc_start: 0.8225 (t0) cc_final: 0.7760 (m-40) REVERT: O 205 CYS cc_start: 0.6638 (OUTLIER) cc_final: 0.6418 (m) REVERT: O 426 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6262 (mmt) outliers start: 57 outliers final: 47 residues processed: 391 average time/residue: 0.1878 time to fit residues: 114.2334 Evaluate side-chains 390 residues out of total 2703 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 339 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 64 GLN Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 90 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain R residue 58 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 196 CYS Chi-restraints excluded: chain G residue 205 CYS Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 584 GLU Chi-restraints excluded: chain H residue 606 THR Chi-restraints excluded: chain H residue 616 ASN Chi-restraints excluded: chain H residue 637 ASN Chi-restraints excluded: chain I residue 17 SER Chi-restraints excluded: chain I residue 18 MET Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 100 GLN Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 95 MET Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 196 CYS Chi-restraints excluded: chain O residue 205 CYS Chi-restraints excluded: chain O residue 320 THR Chi-restraints excluded: chain O residue 364 SER Chi-restraints excluded: chain O residue 426 MET Chi-restraints excluded: chain P residue 520 LEU Chi-restraints excluded: chain P residue 637 ASN Chi-restraints excluded: chain P residue 652 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 39 optimal weight: 20.0000 chunk 293 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.0670 chunk 247 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.163122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112079 restraints weight = 39304.786| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.49 r_work: 0.3239 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27183 Z= 0.176 Angle : 0.618 13.887 37215 Z= 0.299 Chirality : 0.045 0.454 4515 Planarity : 0.004 0.042 4464 Dihedral : 7.237 76.672 6537 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.29 % Allowed : 14.28 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3048 helix: 0.94 (0.24), residues: 453 sheet: 0.11 (0.17), residues: 924 loop : 0.02 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 61 TYR 0.019 0.002 TYR Q 49 PHE 0.012 0.002 PHE J 98 TRP 0.050 0.002 TRP Q 35 HIS 0.004 0.001 HIS O 249 Details of bonding type rmsd covalent geometry : bond 0.00419 (26979) covalent geometry : angle 0.57996 (36651) SS BOND : bond 0.00378 ( 48) SS BOND : angle 1.78339 ( 96) hydrogen bonds : bond 0.03792 ( 767) hydrogen bonds : angle 5.45147 ( 1935) link_ALPHA1-2 : bond 0.00613 ( 9) link_ALPHA1-2 : angle 1.50138 ( 27) link_ALPHA1-3 : bond 0.00841 ( 12) link_ALPHA1-3 : angle 1.41001 ( 36) link_ALPHA1-6 : bond 0.00566 ( 15) link_ALPHA1-6 : angle 1.61076 ( 45) link_BETA1-4 : bond 0.00417 ( 57) link_BETA1-4 : angle 1.74284 ( 171) link_NAG-ASN : bond 0.00346 ( 63) link_NAG-ASN : angle 2.08362 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6902.73 seconds wall clock time: 119 minutes 11.16 seconds (7151.16 seconds total)