Starting phenix.real_space_refine on Thu Nov 20 09:11:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cuf_7622/11_2025/6cuf_7622_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cuf_7622/11_2025/6cuf_7622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cuf_7622/11_2025/6cuf_7622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cuf_7622/11_2025/6cuf_7622.map" model { file = "/net/cci-nas-00/data/ceres_data/6cuf_7622/11_2025/6cuf_7622_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cuf_7622/11_2025/6cuf_7622_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 sd= 0.127 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 162 5.16 5 C 20319 2.51 5 N 5319 2.21 5 O 6525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32325 Number of models: 1 Model: "" Number of chains: 72 Chain: "3" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "4" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "6" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "7" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "8" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "C" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "L" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "Q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "h" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "l" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 882 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 106} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "q" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1023 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "2" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "A" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "c" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "d" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3565 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: "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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 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: "K" 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 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: "f" 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: "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: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "k" Number of atoms: 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: 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: "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: "s" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "t" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "u" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "v" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "w" Number of atoms: 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: 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: "y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "z" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "9" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "AA" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "BA" Number of atoms: 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: "CA" 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: "DA" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 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: "D" 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: "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: "A" 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: "c" 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: "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 Time building chain proxies: 7.82, per 1000 atoms: 0.24 Number of scatterers: 32325 At special positions: 0 Unit cell: (155.82, 162.18, 154.76, 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 162 16.00 O 6525 8.00 N 5319 7.00 C 20319 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 93 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 22 " - pdb=" SG CYS 8 92 " distance=2.04 Simple disulfide: pdb=" SG CYS 8 98 " - pdb=" SG CYS 8 100A" distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.02 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 98 " - pdb=" SG CYS Q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 93 " distance=2.04 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.04 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.02 Simple disulfide: pdb=" SG CYS c 598 " - pdb=" SG CYS c 604 " distance=2.02 Simple disulfide: pdb=" SG CYS d 119 " - pdb=" SG CYS d 205 " distance=2.02 Simple disulfide: pdb=" SG CYS d 126 " - pdb=" SG CYS d 196 " distance=2.03 Simple disulfide: pdb=" SG CYS d 131 " - pdb=" SG CYS d 157 " distance=2.04 Simple disulfide: pdb=" SG CYS d 218 " - pdb=" SG CYS d 247 " distance=2.03 Simple disulfide: pdb=" SG CYS d 228 " - pdb=" SG CYS d 239 " distance=2.04 Simple disulfide: pdb=" SG CYS d 296 " - pdb=" SG CYS d 331 " distance=2.02 Simple disulfide: pdb=" SG CYS d 378 " - pdb=" SG CYS d 445 " distance=2.03 Simple disulfide: pdb=" SG CYS d 385 " - pdb=" SG CYS d 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM31616 O5 NAG u 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30971 O5 NAG Y 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31733 O5 NAG x 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30443 O5 NAG I 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31088 O5 NAG b 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31021 O5 NAG Z 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30376 O5 NAG F 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31666 O5 NAG v 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32000 O5 NAGAA 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30710 O5 NAG T 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31355 O5 NAG k 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30326 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31872 O5 NAG 0 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM30582 O5 NAG O 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM31227 O5 NAG g 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM32225 O5 NAG C 628 .*. O " rejected from bonding due to valence issues. Atom "HETATM32323 O5 NAG d 628 .*. O " rejected from bonding due to valence issues. Atom "HETATM32267 O5 NAG 2 628 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN e 4 " - " MAN e 5 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " " MAN y 4 " - " MAN y 5 " " MANBA 4 " - " MANBA 5 " " MANBA 5 " - " MANBA 6 " ALPHA1-3 " BMA 9 3 " - " MAN 9 4 " " BMA B 3 " - " MAN B 4 " " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " MAN U 7 " - " MAN U 8 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA e 3 " - " MAN e 4 " " BMA j 3 " - " MAN j 4 " " BMA o 3 " - " MAN o 4 " " MAN o 7 " - " MAN o 8 " " BMA s 3 " - " MAN s 4 " " BMA t 3 " - " MAN t 4 " " BMA u 3 " - " MAN u 4 " " BMA y 3 " - " MAN y 4 " " BMABA 3 " - " MANBA 4 " " MANBA 7 " - " MANBA 8 " " BMADA 3 " - " MANDA 4 " ALPHA1-6 " BMA 9 3 " - " MAN 9 5 " " BMA J 3 " - " MAN J 6 " " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 7 " " MAN U 7 " - " MAN U 9 " " BMA e 3 " - " MAN e 6 " " BMA j 3 " - " MAN j 5 " " BMA o 3 " - " MAN o 7 " " MAN o 7 " - " MAN o 9 " " BMA y 3 " - " MAN y 6 " " BMABA 3 " - " MANBA 7 " " MANBA 7 " - " MANBA 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 9 1 " - " NAG 9 2 " " NAG 9 2 " - " BMA 9 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG v 2 " - " BMA v 3 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " NAG-ASN " NAG 0 1 " - " ASN d 301 " " NAG 1 1 " - " ASN d 363 " " NAG 2 601 " - " ASN 2 133 " " NAG 2 628 " - " ASN 2 355 " " NAG 9 1 " - " ASN d 386 " " NAG A 701 " - " ASN A 637 " " NAG B 1 " - " ASN C 137 " " NAG C 601 " - " ASN C 133 " " NAG C 628 " - " ASN C 355 " " NAG D 701 " - " ASN D 637 " " NAG E 1 " - " ASN C 156 " " NAG F 1 " - " ASN C 160 " " NAG G 1 " - " ASN C 197 " " NAG I 1 " - " ASN C 234 " " NAG J 1 " - " ASN C 262 " " NAG K 1 " - " ASN C 295 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 363 " " NAG S 1 " - " ASN C 386 " " NAG T 1 " - " ASN C 392 " " NAG U 1 " - " ASN C 332 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN 2 137 " " NAG Y 1 " - " ASN 2 156 " " NAG Z 1 " - " ASN 2 160 " " NAG a 1 " - " ASN 2 197 " " NAG b 1 " - " ASN 2 234 " " NAG c 701 " - " ASN c 637 " " NAG d 601 " - " ASN d 133 " " NAG d 628 " - " ASN d 355 " " NAG e 1 " - " ASN 2 262 " " NAG f 1 " - " ASN 2 295 " " NAG g 1 " - " ASN 2 301 " " NAG i 1 " - " ASN 2 363 " " NAG j 1 " - " ASN 2 386 " " NAG k 1 " - " ASN 2 392 " " NAG o 1 " - " ASN 2 332 " " NAG p 1 " - " ASN 2 448 " " NAG s 1 " - " ASN 2 276 " " NAG t 1 " - " ASN d 137 " " NAG u 1 " - " ASN d 156 " " NAG v 1 " - " ASN d 160 " " NAG w 1 " - " ASN d 197 " " NAG x 1 " - " ASN d 234 " " NAG y 1 " - " ASN d 262 " " NAG z 1 " - " ASN d 295 " " NAGAA 1 " - " ASN d 392 " " NAGBA 1 " - " ASN d 332 " " NAGCA 1 " - " ASN d 448 " " NAGDA 1 " - " ASN d 276 " Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 82 sheets defined 15.9% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain '3' and resid 28 through 32 removed outlier: 4.191A pdb=" N ASP 3 31 " --> pdb=" O THR 3 28 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR 3 32 " --> pdb=" O PHE 3 29 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 28 through 32' Processing helix chain '3' and resid 83 through 87 Processing helix chain '5' and resid 83 through 87 removed outlier: 3.592A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '5' and resid 100D through 100H Processing helix chain '6' and resid 79 through 83 Processing helix chain '7' and resid 79 through 83 Processing helix chain '8' and resid 61 through 64 Processing helix chain '8' and resid 83 through 87 Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.527A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.733A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 4.017A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.720A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'D' and resid 514 through 520 removed outlier: 4.394A pdb=" N VAL D 518 " --> pdb=" O GLY D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.629A pdb=" N ALA D 526 " --> pdb=" O LEU D 523 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 523 through 527' Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 546 removed outlier: 3.662A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 removed outlier: 4.016A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.048A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.538A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 640 through 664 removed outlier: 3.709A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.168A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 83 through 87 removed outlier: 3.551A pdb=" N THR Q 87 " --> pdb=" O PRO Q 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'h' and resid 28 through 32 removed outlier: 4.135A pdb=" N ASP h 31 " --> pdb=" O THR h 28 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR h 32 " --> pdb=" O PHE h 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 28 through 32' Processing helix chain 'h' and resid 83 through 87 Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.671A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 79 through 83 Processing helix chain 'q' and resid 61 through 64 Processing helix chain 'q' and resid 83 through 87 Processing helix chain 'r' and resid 79 through 83 Processing helix chain '2' and resid 58 through 63 removed outlier: 3.526A pdb=" N THR 2 63 " --> pdb=" O LYS 2 59 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 115 removed outlier: 3.733A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 123 through 126 removed outlier: 4.017A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 123 through 126' Processing helix chain '2' and resid 177 through 179 No H-bonds generated for 'chain '2' and resid 177 through 179' Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 removed outlier: 3.719A pdb=" N THR 2 373 " --> pdb=" O LEU 2 369 " (cutoff:3.500A) Processing helix chain '2' and resid 475 through 481 Processing helix chain '2' and resid 482 through 484 No H-bonds generated for 'chain '2' and resid 482 through 484' Processing helix chain 'A' and resid 514 through 520 removed outlier: 4.395A pdb=" N VAL A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.629A pdb=" N ALA A 526 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 527' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 546 removed outlier: 3.662A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 595 removed outlier: 4.017A pdb=" N LYS A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.047A pdb=" N SER A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.538A pdb=" N ILE A 622 " --> pdb=" O ASN A 618 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 640 through 664 removed outlier: 3.709A pdb=" N GLY A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'c' and resid 514 through 520 removed outlier: 4.394A pdb=" N VAL c 518 " --> pdb=" O GLY c 514 " (cutoff:3.500A) Processing helix chain 'c' and resid 523 through 527 removed outlier: 3.630A pdb=" N ALA c 526 " --> pdb=" O LEU c 523 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY c 527 " --> pdb=" O GLY c 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 523 through 527' Processing helix chain 'c' and resid 529 through 534 Processing helix chain 'c' and resid 537 through 546 removed outlier: 3.662A pdb=" N LEU c 545 " --> pdb=" O ALA c 541 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER c 546 " --> pdb=" O ARG c 542 " (cutoff:3.500A) Processing helix chain 'c' and resid 570 through 595 removed outlier: 4.016A pdb=" N LYS c 574 " --> pdb=" O VAL c 570 " (cutoff:3.500A) Processing helix chain 'c' and resid 611 through 616 removed outlier: 4.048A pdb=" N SER c 615 " --> pdb=" O ASN c 611 " (cutoff:3.500A) Processing helix chain 'c' and resid 618 through 626 removed outlier: 3.538A pdb=" N ILE c 622 " --> pdb=" O ASN c 618 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP c 623 " --> pdb=" O LEU c 619 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP c 624 " --> pdb=" O SER c 620 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET c 626 " --> pdb=" O ILE c 622 " (cutoff:3.500A) Processing helix chain 'c' and resid 627 through 636 Processing helix chain 'c' and resid 640 through 664 removed outlier: 3.709A pdb=" N GLY c 644 " --> pdb=" O GLN c 640 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 63 removed outlier: 3.526A pdb=" N THR d 63 " --> pdb=" O LYS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 115 removed outlier: 3.734A pdb=" N ILE d 109 " --> pdb=" O HIS d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 126 removed outlier: 4.018A pdb=" N CYS d 126 " --> pdb=" O THR d 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 123 through 126' Processing helix chain 'd' and resid 177 through 179 No H-bonds generated for 'chain 'd' and resid 177 through 179' Processing helix chain 'd' and resid 195 through 198 Processing helix chain 'd' and resid 335 through 350 Processing helix chain 'd' and resid 368 through 373 removed outlier: 3.720A pdb=" N THR d 373 " --> pdb=" O LEU d 369 " (cutoff:3.500A) Processing helix chain 'd' and resid 475 through 481 Processing helix chain 'd' and resid 482 through 484 No H-bonds generated for 'chain 'd' and resid 482 through 484' Processing sheet with id=AA1, first strand: chain '3' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain '3' and resid 10 through 11 removed outlier: 6.663A pdb=" N GLU 3 10 " --> pdb=" O THR 3 110 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE 3 34 " --> pdb=" O ALA 3 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA 3 50 " --> pdb=" O ILE 3 34 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain '4' and resid 10 through 12 removed outlier: 6.405A pdb=" N LEU 4 11 " --> pdb=" O GLU 4 110 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY 4 89 " --> pdb=" O LEU 4 109 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU 4 42 " --> pdb=" O LEU 4 51 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU 4 51 " --> pdb=" O LEU 4 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '4' and resid 10 through 12 removed outlier: 6.405A pdb=" N LEU 4 11 " --> pdb=" O GLU 4 110 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY 4 89 " --> pdb=" O LEU 4 109 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR 4 102 " --> pdb=" O GLN 4 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 5 through 7 Processing sheet with id=AA7, first strand: chain '5' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain '5' and resid 46 through 51 removed outlier: 5.074A pdb=" N TRP 5 47 " --> pdb=" O ARG 5 38 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG 5 38 " --> pdb=" O TRP 5 47 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR 5 90 " --> pdb=" O THR 5 105 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR 5 105 " --> pdb=" O TYR 5 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 96 through 100A removed outlier: 3.754A pdb=" N GLY 5 98 " --> pdb=" O TYR 5 100M" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '6' and resid 9 through 13 removed outlier: 5.786A pdb=" N VAL 6 11 " --> pdb=" O ILE 6 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR 6 102 " --> pdb=" O TYR 6 86 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLN 6 37 " --> pdb=" O LEU 6 46 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU 6 46 " --> pdb=" O GLN 6 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '6' and resid 19 through 26 removed outlier: 3.621A pdb=" N ALA 6 71 " --> pdb=" O CYS 6 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '7' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain '7' and resid 10 through 13 removed outlier: 6.012A pdb=" N GLN 7 37 " --> pdb=" O LEU 7 46 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU 7 46 " --> pdb=" O GLN 7 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain '8' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain '8' and resid 10 through 11 removed outlier: 6.779A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG 8 38 " --> pdb=" O TRP 8 47 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TRP 8 47 " --> pdb=" O ARG 8 38 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE 8 40 " --> pdb=" O PHE 8 45 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE 8 45 " --> pdb=" O ILE 8 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '8' and resid 10 through 11 removed outlier: 6.779A pdb=" N VAL 8 10 " --> pdb=" O VAL 8 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.515A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.620A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 120 through 121 removed outlier: 3.836A pdb=" N VAL C 120 " --> pdb=" O GLN C 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'C' and resid 181 through 184 removed outlier: 4.589A pdb=" N GLU C 190 " --> pdb=" O ILE C 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.299A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS C 374 " --> pdb=" O CYS C 385 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.570A pdb=" N PHE C 288 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 304 through 306 Processing sheet with id=AD1, first strand: chain 'C' and resid 359 through 360 Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.727A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.391A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY L 89 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU L 42 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU L 51 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.391A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY L 89 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AD8, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AD9, first strand: chain 'M' and resid 46 through 51 removed outlier: 5.062A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR M 95 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY M 98 " --> pdb=" O TYR M 100M" (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 9 through 13 removed outlier: 5.877A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR N 102 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 19 through 26 removed outlier: 3.614A pdb=" N ALA N 71 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.730A pdb=" N VAL Q 10 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE Q 40 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE Q 45 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 10 through 11 removed outlier: 6.730A pdb=" N VAL Q 10 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.495A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'h' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'h' and resid 10 through 11 removed outlier: 6.989A pdb=" N ILE h 34 " --> pdb=" O ALA h 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA h 50 " --> pdb=" O ILE h 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TRP h 36 " --> pdb=" O ILE h 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'l' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU l 11 " --> pdb=" O GLU l 110 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY l 89 " --> pdb=" O LEU l 109 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU l 42 " --> pdb=" O LEU l 51 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU l 51 " --> pdb=" O LEU l 42 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU l 11 " --> pdb=" O GLU l 110 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY l 89 " --> pdb=" O LEU l 109 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR l 102 " --> pdb=" O GLN l 95 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'm' and resid 5 through 7 Processing sheet with id=AF6, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.695A pdb=" N THR m 95 " --> pdb=" O TYR m 33 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR m 33 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY m 49 " --> pdb=" O TRP m 36 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG m 38 " --> pdb=" O TRP m 47 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TRP m 47 " --> pdb=" O ARG m 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.799A pdb=" N GLY m 98 " --> pdb=" O TYR m 100M" (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'n' and resid 9 through 13 removed outlier: 5.922A pdb=" N VAL n 11 " --> pdb=" O ILE n 105 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLN n 37 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU n 46 " --> pdb=" O GLN n 37 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'n' and resid 19 through 26 removed outlier: 3.694A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AG2, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AG3, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.621A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY q 49 " --> pdb=" O TRP q 36 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.621A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'r' and resid 5 through 6 Processing sheet with id=AG6, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.534A pdb=" N TRP r 35 " --> pdb=" O LEU r 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '2' and resid 35 through 39 Processing sheet with id=AG8, first strand: chain '2' and resid 45 through 47 removed outlier: 3.515A pdb=" N LYS 2 487 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '2' and resid 75 through 76 Processing sheet with id=AH1, first strand: chain '2' and resid 91 through 94 removed outlier: 3.620A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '2' and resid 120 through 121 removed outlier: 3.837A pdb=" N VAL 2 120 " --> pdb=" O GLN 2 203 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '2' and resid 130 through 133 Processing sheet with id=AH4, first strand: chain '2' and resid 181 through 184 removed outlier: 4.590A pdb=" N GLU 2 190 " --> pdb=" O ILE 2 184 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '2' and resid 271 through 273 removed outlier: 7.299A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS 2 374 " --> pdb=" O CYS 2 385 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2' and resid 271 through 273 removed outlier: 3.570A pdb=" N PHE 2 288 " --> pdb=" O THR 2 450 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR 2 450 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N THR 2 290 " --> pdb=" O ASN 2 448 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N ASN 2 448 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N VAL 2 292 " --> pdb=" O VAL 2 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL 2 446 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N ILE 2 294 " --> pdb=" O ARG 2 444 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ARG 2 444 " --> pdb=" O ILE 2 294 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N CYS 2 296 " --> pdb=" O VAL 2 442 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N VAL 2 442 " --> pdb=" O CYS 2 296 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '2' and resid 304 through 306 Processing sheet with id=AH8, first strand: chain '2' and resid 359 through 360 Processing sheet with id=AH9, first strand: chain 'd' and resid 35 through 39 Processing sheet with id=AI1, first strand: chain 'd' and resid 45 through 47 removed outlier: 3.515A pdb=" N LYS d 487 " --> pdb=" O LEU d 226 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE d 225 " --> pdb=" O VAL d 245 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'd' and resid 75 through 76 Processing sheet with id=AI3, first strand: chain 'd' and resid 91 through 94 removed outlier: 3.620A pdb=" N GLU d 91 " --> pdb=" O CYS d 239 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'd' and resid 120 through 121 removed outlier: 3.837A pdb=" N VAL d 120 " --> pdb=" O GLN d 203 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'd' and resid 130 through 133 Processing sheet with id=AI6, first strand: chain 'd' and resid 181 through 184 removed outlier: 4.590A pdb=" N GLU d 190 " --> pdb=" O ILE d 184 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'd' and resid 271 through 273 removed outlier: 7.299A pdb=" N GLN d 293 " --> pdb=" O SER d 334 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER d 334 " --> pdb=" O GLN d 293 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS d 374 " --> pdb=" O CYS d 385 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'd' and resid 271 through 273 removed outlier: 3.570A pdb=" N PHE d 288 " --> pdb=" O THR d 450 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR d 450 " --> pdb=" O PHE d 288 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N THR d 290 " --> pdb=" O ASN d 448 " (cutoff:3.500A) removed outlier: 9.320A pdb=" N ASN d 448 " --> pdb=" O THR d 290 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N VAL d 292 " --> pdb=" O VAL d 446 " (cutoff:3.500A) removed outlier: 9.724A pdb=" N VAL d 446 " --> pdb=" O VAL d 292 " (cutoff:3.500A) removed outlier: 11.257A pdb=" N ILE d 294 " --> pdb=" O ARG d 444 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N ARG d 444 " --> pdb=" O ILE d 294 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N CYS d 296 " --> pdb=" O VAL d 442 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N VAL d 442 " --> pdb=" O CYS d 296 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'd' and resid 304 through 306 Processing sheet with id=AJ1, first strand: chain 'd' and resid 359 through 360 1078 hydrogen bonds defined for protein. 2712 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: 8.29 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9612 1.33 - 1.46: 8154 1.46 - 1.58: 15060 1.58 - 1.70: 3 1.70 - 1.82: 216 Bond restraints: 33045 Sorted by residual: bond pdb=" C1 BMA 1 3 " pdb=" C2 BMA 1 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C1 BMA P 3 " pdb=" C2 BMA P 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" C1 BMA i 3 " pdb=" C2 BMA i 3 " ideal model delta sigma weight residual 1.519 1.580 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" C5 MAN J 4 " pdb=" O5 MAN J 4 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" C5 MAN y 4 " pdb=" O5 MAN y 4 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 7.11e+00 ... (remaining 33040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 44304 3.65 - 7.30: 553 7.30 - 10.95: 47 10.95 - 14.61: 0 14.61 - 18.26: 3 Bond angle restraints: 44907 Sorted by residual: angle pdb=" CA LEU 2 494 " pdb=" CB LEU 2 494 " pdb=" CG LEU 2 494 " ideal model delta sigma weight residual 116.30 134.56 -18.26 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU d 494 " pdb=" CB LEU d 494 " pdb=" CG LEU d 494 " ideal model delta sigma weight residual 116.30 134.54 -18.24 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU C 494 " pdb=" CB LEU C 494 " pdb=" CG LEU C 494 " ideal model delta sigma weight residual 116.30 134.53 -18.23 3.50e+00 8.16e-02 2.71e+01 angle pdb=" C ASN 2 99 " pdb=" N MET 2 100 " pdb=" CA MET 2 100 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" C ASN C 99 " pdb=" N MET C 100 " pdb=" CA MET C 100 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.37e+01 ... (remaining 44902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 20486 22.16 - 44.32: 704 44.32 - 66.48: 137 66.48 - 88.65: 144 88.65 - 110.81: 102 Dihedral angle restraints: 21573 sinusoidal: 10551 harmonic: 11022 Sorted by residual: dihedral pdb=" CA LYS 4 55 " pdb=" C LYS 4 55 " pdb=" N VAL 4 56 " pdb=" CA VAL 4 56 " ideal model delta harmonic sigma weight residual -180.00 -140.73 -39.27 0 5.00e+00 4.00e-02 6.17e+01 dihedral pdb=" CA LYS l 55 " pdb=" C LYS l 55 " pdb=" N VAL l 56 " pdb=" CA VAL l 56 " ideal model delta harmonic sigma weight residual 180.00 -140.87 -39.13 0 5.00e+00 4.00e-02 6.13e+01 dihedral pdb=" CA LYS L 55 " pdb=" C LYS L 55 " pdb=" N VAL L 56 " pdb=" CA VAL L 56 " ideal model delta harmonic sigma weight residual 180.00 -141.25 -38.75 0 5.00e+00 4.00e-02 6.01e+01 ... (remaining 21570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.292: 5392 0.292 - 0.584: 27 0.584 - 0.876: 11 0.876 - 1.168: 9 1.168 - 1.460: 3 Chirality restraints: 5442 Sorted by residual: chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN 2 234 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.33e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.32e+01 chirality pdb=" C1 NAG x 1 " pdb=" ND2 ASN d 234 " pdb=" C2 NAG x 1 " pdb=" O5 NAG x 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.94 -1.46 2.00e-01 2.50e+01 5.31e+01 ... (remaining 5439 not shown) Planarity restraints: 5523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 276 " -0.103 2.00e-02 2.50e+03 3.92e-01 1.92e+03 pdb=" CG ASN 2 276 " 0.134 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 276 " -0.190 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 276 " 0.667 2.00e-02 2.50e+03 pdb=" C1 NAG s 1 " -0.508 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 276 " -0.103 2.00e-02 2.50e+03 3.92e-01 1.92e+03 pdb=" CG ASN C 276 " 0.134 2.00e-02 2.50e+03 pdb=" OD1 ASN C 276 " -0.190 2.00e-02 2.50e+03 pdb=" ND2 ASN C 276 " 0.667 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.508 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN d 276 " -0.103 2.00e-02 2.50e+03 3.92e-01 1.92e+03 pdb=" CG ASN d 276 " 0.134 2.00e-02 2.50e+03 pdb=" OD1 ASN d 276 " -0.190 2.00e-02 2.50e+03 pdb=" ND2 ASN d 276 " 0.667 2.00e-02 2.50e+03 pdb=" C1 NAGDA 1 " -0.507 2.00e-02 2.50e+03 ... (remaining 5520 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 408 2.57 - 3.15: 25415 3.15 - 3.73: 48915 3.73 - 4.32: 67968 4.32 - 4.90: 110520 Nonbonded interactions: 253226 Sorted by model distance: nonbonded pdb=" O ASN 2 197 " pdb=" OD1 ASN 2 197 " model vdw 1.984 3.040 nonbonded pdb=" O ASN d 197 " pdb=" OD1 ASN d 197 " model vdw 1.984 3.040 nonbonded pdb=" O ASN C 197 " pdb=" OD1 ASN C 197 " model vdw 1.985 3.040 nonbonded pdb=" OE2 GLU 2 164 " pdb=" NH1 ARG 2 308 " model vdw 2.021 3.120 nonbonded pdb=" OE2 GLU C 164 " pdb=" NH1 ARG C 308 " model vdw 2.021 3.120 ... (remaining 253221 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: 0.02 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'AA' selection = chain 'CA' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'T' selection = chain 'V' selection = chain 'a' selection = chain 'f' selection = chain 'g' selection = chain 'k' selection = chain 'p' selection = chain 'w' selection = chain 'z' } ncs_group { reference = chain '1' selection = chain 'F' selection = chain 'I' selection = chain 'P' selection = chain 'Z' selection = chain 'b' selection = chain 'i' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'd' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '8' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '9' selection = chain 'S' selection = chain 'j' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'c' } ncs_group { reference = chain 'B' selection = chain 'DA' selection = chain 'E' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 's' selection = chain 't' selection = chain 'u' } ncs_group { reference = chain 'BA' selection = chain 'U' selection = chain 'o' } ncs_group { reference = chain 'J' selection = chain 'e' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.780 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 0.009 0.414 33252 Z= 0.434 Angle : 1.776 53.894 45483 Z= 0.710 Chirality : 0.094 1.460 5442 Planarity : 0.007 0.070 5472 Dihedral : 15.872 110.807 14388 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.33 % Favored : 92.59 % Rotamer: Outliers : 0.81 % Allowed : 2.97 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % 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: -3.25 (0.12), residues: 3777 helix: -2.52 (0.19), residues: 480 sheet: -1.42 (0.14), residues: 1203 loop : -2.58 (0.11), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 298 TYR 0.026 0.003 TYR c 638 PHE 0.025 0.003 PHE r 97 TRP 0.038 0.003 TRP Q 103 HIS 0.010 0.003 HIS Q 35 Details of bonding type rmsd covalent geometry : bond 0.00791 (33045) covalent geometry : angle 1.05947 (44907) SS BOND : bond 0.00588 ( 45) SS BOND : angle 1.23481 ( 90) hydrogen bonds : bond 0.09989 ( 1006) hydrogen bonds : angle 7.16867 ( 2712) link_ALPHA1-2 : bond 0.00396 ( 9) link_ALPHA1-2 : angle 2.67689 ( 27) link_ALPHA1-3 : bond 0.00514 ( 21) link_ALPHA1-3 : angle 2.09300 ( 63) link_ALPHA1-6 : bond 0.00524 ( 12) link_ALPHA1-6 : angle 1.83938 ( 36) link_BETA1-4 : bond 0.00995 ( 69) link_BETA1-4 : angle 4.35440 ( 207) link_NAG-ASN : bond 0.11447 ( 51) link_NAG-ASN : angle 24.02799 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 587 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 5 GLN cc_start: 0.9454 (tp40) cc_final: 0.9203 (tm-30) REVERT: 3 33 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7910 (mt-10) REVERT: 4 51 LEU cc_start: 0.2959 (tp) cc_final: 0.0952 (tp) REVERT: 4 77 THR cc_start: 0.7447 (m) cc_final: 0.7167 (m) REVERT: 7 1 GLU cc_start: 0.8680 (pt0) cc_final: 0.8303 (mt-10) REVERT: 7 54 ARG cc_start: 0.8417 (mtm110) cc_final: 0.7925 (ptp90) REVERT: 7 81 GLU cc_start: 0.9244 (mm-30) cc_final: 0.9015 (tp30) REVERT: 8 28 ASN cc_start: 0.8866 (t0) cc_final: 0.8449 (t0) REVERT: 8 39 LEU cc_start: 0.8669 (tp) cc_final: 0.8169 (tt) REVERT: C 52 LEU cc_start: 0.9194 (mt) cc_final: 0.8989 (mt) REVERT: D 654 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8447 (tp30) REVERT: H 100 PHE cc_start: 0.6267 (m-80) cc_final: 0.5879 (m-80) REVERT: L 67 PHE cc_start: 0.7175 (m-80) cc_final: 0.6700 (m-80) REVERT: L 77 THR cc_start: 0.8084 (m) cc_final: 0.7884 (p) REVERT: N 90 ILE cc_start: 0.9123 (pt) cc_final: 0.8900 (mt) REVERT: Q 73 LEU cc_start: 0.8668 (mt) cc_final: 0.8175 (mt) REVERT: Q 100 TYR cc_start: 0.9151 (m-80) cc_final: 0.8570 (m-10) REVERT: R 1 GLU cc_start: 0.8739 (pt0) cc_final: 0.7983 (mt-10) REVERT: R 81 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8933 (tp30) REVERT: h 86 ASP cc_start: 0.7311 (m-30) cc_final: 0.6981 (m-30) REVERT: h 100 PHE cc_start: 0.6291 (m-80) cc_final: 0.5773 (m-80) REVERT: q 28 ASN cc_start: 0.8816 (t0) cc_final: 0.8432 (t0) REVERT: q 100 TYR cc_start: 0.9213 (m-80) cc_final: 0.8690 (m-10) REVERT: r 1 GLU cc_start: 0.8766 (pt0) cc_final: 0.8474 (mt-10) REVERT: 2 100 MET cc_start: 0.8748 (ptp) cc_final: 0.8483 (ptp) REVERT: A 652 GLN cc_start: 0.9374 (tt0) cc_final: 0.8666 (tp-100) REVERT: c 535 MET cc_start: 0.9118 (mmt) cc_final: 0.8558 (mmt) REVERT: c 654 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8514 (tp30) outliers start: 27 outliers final: 10 residues processed: 611 average time/residue: 0.2591 time to fit residues: 235.2275 Evaluate side-chains 280 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 270 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain 2 residue 197 ASN Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 332 ASN Chi-restraints excluded: chain 2 residue 392 ASN Chi-restraints excluded: chain d residue 197 ASN Chi-restraints excluded: chain d residue 332 ASN Chi-restraints excluded: chain d residue 392 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 8.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 35 HIS 3 43 HIS ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 97 ASN 4 27 GLN ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 58 ASN 8 6 GLN C 82 GLN C 249 HIS C 293 GLN C 374 HIS D 611 ASN ** D 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS H 39 GLN L 35 ASN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN M 97 HIS N 95CASN Q 101 GLN h 35 HIS h 39 GLN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 97 ASN l 27 GLN l 58 ASN n 95CASN 2 82 GLN 2 249 HIS 2 293 GLN 2 374 HIS A 611 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 577 GLN c 611 ASN ** c 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 GLN d 249 HIS d 293 GLN d 374 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.059506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.042642 restraints weight = 201427.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.043673 restraints weight = 109887.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.044361 restraints weight = 79283.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044619 restraints weight = 65780.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.044873 restraints weight = 60070.718| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 33252 Z= 0.303 Angle : 0.916 14.647 45483 Z= 0.424 Chirality : 0.050 0.290 5442 Planarity : 0.006 0.060 5472 Dihedral : 14.553 84.515 7453 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.10 % Allowed : 8.89 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.60 (0.13), residues: 3777 helix: -1.26 (0.23), residues: 444 sheet: -1.31 (0.14), residues: 1185 loop : -2.10 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 8 61 TYR 0.020 0.002 TYR d 318 PHE 0.014 0.002 PHE C 288 TRP 0.017 0.002 TRP 3 99 HIS 0.008 0.002 HIS d 330 Details of bonding type rmsd covalent geometry : bond 0.00650 (33045) covalent geometry : angle 0.84753 (44907) SS BOND : bond 0.00301 ( 45) SS BOND : angle 0.96778 ( 90) hydrogen bonds : bond 0.04382 ( 1006) hydrogen bonds : angle 6.74392 ( 2712) link_ALPHA1-2 : bond 0.00697 ( 9) link_ALPHA1-2 : angle 2.13103 ( 27) link_ALPHA1-3 : bond 0.00622 ( 21) link_ALPHA1-3 : angle 2.73913 ( 63) link_ALPHA1-6 : bond 0.00378 ( 12) link_ALPHA1-6 : angle 1.97531 ( 36) link_BETA1-4 : bond 0.00754 ( 69) link_BETA1-4 : angle 3.16267 ( 207) link_NAG-ASN : bond 0.00865 ( 51) link_NAG-ASN : angle 4.42475 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 297 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 5 GLN cc_start: 0.9413 (tp40) cc_final: 0.9181 (tm-30) REVERT: 3 62 LYS cc_start: 0.9202 (tppt) cc_final: 0.8810 (ttpp) REVERT: 7 1 GLU cc_start: 0.9119 (pt0) cc_final: 0.8424 (mt-10) REVERT: 7 39 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8297 (mtp85) REVERT: 7 81 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8680 (tm-30) REVERT: 8 3 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8592 (mm110) REVERT: 8 28 ASN cc_start: 0.9325 (t0) cc_final: 0.9004 (t0) REVERT: D 652 GLN cc_start: 0.9349 (tt0) cc_final: 0.8794 (tp-100) REVERT: D 664 ASP cc_start: 0.7888 (m-30) cc_final: 0.7593 (p0) REVERT: H 48 ILE cc_start: 0.4866 (mt) cc_final: 0.4653 (mt) REVERT: H 66 LYS cc_start: 0.7372 (ptmt) cc_final: 0.6698 (tptp) REVERT: H 86 ASP cc_start: 0.8275 (m-30) cc_final: 0.7986 (m-30) REVERT: H 100 PHE cc_start: 0.7075 (m-80) cc_final: 0.6655 (m-80) REVERT: L 59 ARG cc_start: 0.7539 (mpt-90) cc_final: 0.7328 (mpt-90) REVERT: M 100 MET cc_start: 0.8853 (mmm) cc_final: 0.8480 (mmm) REVERT: Q 73 LEU cc_start: 0.8787 (mt) cc_final: 0.8496 (mt) REVERT: Q 80 MET cc_start: 0.8816 (tmm) cc_final: 0.8595 (tmm) REVERT: R 54 ARG cc_start: 0.8502 (mtm110) cc_final: 0.7855 (mtp180) REVERT: R 81 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8871 (tp30) REVERT: h 62 LYS cc_start: 0.9170 (tppt) cc_final: 0.8773 (ttpp) REVERT: h 86 ASP cc_start: 0.7362 (m-30) cc_final: 0.7074 (m-30) REVERT: h 98 TYR cc_start: 0.8803 (m-80) cc_final: 0.8101 (m-80) REVERT: h 100 PHE cc_start: 0.6794 (m-80) cc_final: 0.6171 (m-80) REVERT: q 28 ASN cc_start: 0.9343 (t0) cc_final: 0.8787 (t0) REVERT: q 31 ASP cc_start: 0.8689 (m-30) cc_final: 0.7908 (m-30) REVERT: q 73 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8113 (tp) REVERT: r 1 GLU cc_start: 0.9104 (pt0) cc_final: 0.8556 (mt-10) REVERT: r 81 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8795 (tp30) REVERT: 2 100 MET cc_start: 0.9311 (ptp) cc_final: 0.9018 (ptp) REVERT: 2 161 MET cc_start: 0.9566 (tpp) cc_final: 0.9316 (tpp) REVERT: 2 265 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8659 (pp) REVERT: A 530 MET cc_start: 0.8228 (ptp) cc_final: 0.7933 (ptp) REVERT: A 652 GLN cc_start: 0.9365 (tt0) cc_final: 0.8760 (tp-100) REVERT: A 654 GLU cc_start: 0.8839 (tp30) cc_final: 0.7902 (tp30) REVERT: c 652 GLN cc_start: 0.9339 (tt0) cc_final: 0.8799 (tp-100) REVERT: c 654 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9064 (tm-30) REVERT: c 664 ASP cc_start: 0.7979 (m-30) cc_final: 0.7655 (p0) REVERT: d 100 MET cc_start: 0.9341 (ptm) cc_final: 0.9036 (ppp) REVERT: d 104 MET cc_start: 0.8765 (tmm) cc_final: 0.8559 (tmm) outliers start: 70 outliers final: 38 residues processed: 348 average time/residue: 0.2183 time to fit residues: 119.6447 Evaluate side-chains 272 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 23 LYS Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 4 residue 102 THR Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 43 HIS Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain q residue 73 LEU Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 194 ILE Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 265 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain c residue 587 LEU Chi-restraints excluded: chain c residue 595 ILE Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 21 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 chunk 186 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 333 optimal weight: 0.4980 chunk 235 optimal weight: 0.6980 chunk 273 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 39 GLN 4 35 ASN ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 ASN 8 101 GLN D 630 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 35 ASN L 47 GLN N 95CASN Q 6 GLN q 6 GLN A 630 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 577 GLN c 630 GLN ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.060689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.043852 restraints weight = 194928.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.044961 restraints weight = 104991.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045724 restraints weight = 74126.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.046032 restraints weight = 61168.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.046325 restraints weight = 55791.132| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 33252 Z= 0.156 Angle : 0.765 15.526 45483 Z= 0.356 Chirality : 0.047 0.270 5442 Planarity : 0.005 0.058 5472 Dihedral : 12.268 85.229 7435 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.43 % Allowed : 9.70 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.23 (0.13), residues: 3777 helix: -0.87 (0.24), residues: 441 sheet: -1.09 (0.14), residues: 1218 loop : -1.88 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 8 61 TYR 0.019 0.001 TYR 4 54 PHE 0.015 0.001 PHE d 288 TRP 0.011 0.001 TRP Q 100F HIS 0.003 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00343 (33045) covalent geometry : angle 0.71111 (44907) SS BOND : bond 0.00269 ( 45) SS BOND : angle 1.71086 ( 90) hydrogen bonds : bond 0.03754 ( 1006) hydrogen bonds : angle 6.18343 ( 2712) link_ALPHA1-2 : bond 0.00548 ( 9) link_ALPHA1-2 : angle 2.03448 ( 27) link_ALPHA1-3 : bond 0.00884 ( 21) link_ALPHA1-3 : angle 1.89012 ( 63) link_ALPHA1-6 : bond 0.00531 ( 12) link_ALPHA1-6 : angle 1.71999 ( 36) link_BETA1-4 : bond 0.00675 ( 69) link_BETA1-4 : angle 2.89566 ( 207) link_NAG-ASN : bond 0.00381 ( 51) link_NAG-ASN : angle 3.06565 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 291 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9274 (tppt) cc_final: 0.8929 (ttpp) REVERT: 5 100 MET cc_start: 0.8814 (mmm) cc_final: 0.8562 (mmm) REVERT: 7 1 GLU cc_start: 0.9063 (pt0) cc_final: 0.8253 (mt-10) REVERT: 7 33 MET cc_start: 0.8543 (tpp) cc_final: 0.8281 (tpp) REVERT: 7 39 ARG cc_start: 0.8579 (mtm-85) cc_final: 0.7790 (mtp85) REVERT: 7 60 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8382 (t0) REVERT: 7 81 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8554 (tp30) REVERT: 8 28 ASN cc_start: 0.9299 (t0) cc_final: 0.8687 (t0) REVERT: 8 31 ASP cc_start: 0.8631 (m-30) cc_final: 0.7958 (m-30) REVERT: 8 43 LYS cc_start: 0.9384 (mmmm) cc_final: 0.9040 (mmmm) REVERT: 8 80 MET cc_start: 0.8804 (tmm) cc_final: 0.8549 (tmm) REVERT: C 104 MET cc_start: 0.8932 (tmm) cc_final: 0.8627 (tmm) REVERT: C 425 ASN cc_start: 0.8636 (t0) cc_final: 0.8144 (t0) REVERT: D 530 MET cc_start: 0.8019 (ptp) cc_final: 0.7660 (ptp) REVERT: D 584 GLU cc_start: 0.8743 (tt0) cc_final: 0.8408 (tm-30) REVERT: H 66 LYS cc_start: 0.7362 (ptmt) cc_final: 0.6791 (tptp) REVERT: H 86 ASP cc_start: 0.8259 (m-30) cc_final: 0.7927 (m-30) REVERT: H 100 PHE cc_start: 0.7152 (m-80) cc_final: 0.6477 (m-80) REVERT: M 82 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8398 (mp) REVERT: M 100 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7947 (mt-10) REVERT: M 100 MET cc_start: 0.8813 (mmm) cc_final: 0.8530 (mmm) REVERT: Q 3 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8433 (mm-40) REVERT: Q 39 LEU cc_start: 0.8874 (pp) cc_final: 0.7803 (pp) REVERT: Q 69 MET cc_start: 0.9074 (mtt) cc_final: 0.8745 (mtm) REVERT: Q 73 LEU cc_start: 0.8703 (mt) cc_final: 0.8465 (mt) REVERT: Q 80 MET cc_start: 0.8850 (tmm) cc_final: 0.8601 (tmm) REVERT: Q 99 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8152 (p0) REVERT: Q 100 TYR cc_start: 0.8707 (m-80) cc_final: 0.8260 (m-10) REVERT: Q 100 ASP cc_start: 0.7514 (p0) cc_final: 0.6650 (t0) REVERT: R 54 ARG cc_start: 0.8614 (mtm110) cc_final: 0.8259 (mtp180) REVERT: R 81 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8793 (tp30) REVERT: h 86 ASP cc_start: 0.7408 (m-30) cc_final: 0.7100 (m-30) REVERT: h 94 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.6173 (ttp-110) REVERT: h 98 TYR cc_start: 0.8720 (m-80) cc_final: 0.7999 (m-80) REVERT: h 100 PHE cc_start: 0.6824 (m-80) cc_final: 0.6191 (m-80) REVERT: l 47 GLN cc_start: 0.7843 (mt0) cc_final: 0.7633 (mp10) REVERT: q 1 GLN cc_start: 0.7694 (pp30) cc_final: 0.7474 (pp30) REVERT: q 3 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8516 (mm-40) REVERT: q 28 ASN cc_start: 0.9323 (t0) cc_final: 0.8687 (t0) REVERT: q 31 ASP cc_start: 0.8681 (m-30) cc_final: 0.8255 (m-30) REVERT: q 76 ASP cc_start: 0.9100 (t0) cc_final: 0.8883 (t0) REVERT: q 80 MET cc_start: 0.8845 (tmm) cc_final: 0.8518 (tmm) REVERT: q 100 ASP cc_start: 0.7558 (p0) cc_final: 0.6764 (t0) REVERT: r 1 GLU cc_start: 0.9112 (pt0) cc_final: 0.8529 (mt-10) REVERT: r 81 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8729 (tp30) REVERT: 2 104 MET cc_start: 0.8982 (tmm) cc_final: 0.8399 (tmm) REVERT: 2 161 MET cc_start: 0.9593 (tpp) cc_final: 0.9382 (tpp) REVERT: A 530 MET cc_start: 0.8128 (ptp) cc_final: 0.7827 (ptp) REVERT: A 584 GLU cc_start: 0.8725 (tt0) cc_final: 0.8456 (tm-30) REVERT: A 652 GLN cc_start: 0.9322 (tt0) cc_final: 0.8705 (tp-100) REVERT: c 584 GLU cc_start: 0.8704 (tt0) cc_final: 0.8356 (tm-30) REVERT: c 652 GLN cc_start: 0.9335 (tt0) cc_final: 0.8790 (tp-100) REVERT: c 654 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8977 (tm-30) REVERT: d 434 MET cc_start: 0.9106 (ttm) cc_final: 0.8894 (ttp) outliers start: 81 outliers final: 41 residues processed: 352 average time/residue: 0.2169 time to fit residues: 122.1950 Evaluate side-chains 292 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 51 THR Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 577 GLN Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 116 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 343 optimal weight: 0.4980 chunk 108 optimal weight: 0.0470 chunk 268 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 overall best weight: 1.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN L 58 ASN M 23 ASN R 6 GLN q 101 GLN 2 428 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 630 GLN ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 428 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.061035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.044254 restraints weight = 193019.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.045350 restraints weight = 103851.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046104 restraints weight = 73511.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.046420 restraints weight = 60490.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046844 restraints weight = 54980.750| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 33252 Z= 0.131 Angle : 0.730 15.799 45483 Z= 0.338 Chirality : 0.046 0.227 5442 Planarity : 0.004 0.061 5472 Dihedral : 10.769 83.081 7435 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.13 % Allowed : 11.08 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.13), residues: 3777 helix: -0.61 (0.24), residues: 441 sheet: -0.92 (0.14), residues: 1257 loop : -1.73 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 8 61 TYR 0.019 0.001 TYR L 91 PHE 0.015 0.001 PHE Q 91 TRP 0.010 0.001 TRP q 100F HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00286 (33045) covalent geometry : angle 0.68154 (44907) SS BOND : bond 0.00352 ( 45) SS BOND : angle 1.90394 ( 90) hydrogen bonds : bond 0.03471 ( 1006) hydrogen bonds : angle 5.89340 ( 2712) link_ALPHA1-2 : bond 0.00509 ( 9) link_ALPHA1-2 : angle 1.98966 ( 27) link_ALPHA1-3 : bond 0.00885 ( 21) link_ALPHA1-3 : angle 1.96744 ( 63) link_ALPHA1-6 : bond 0.00635 ( 12) link_ALPHA1-6 : angle 1.66530 ( 36) link_BETA1-4 : bond 0.00604 ( 69) link_BETA1-4 : angle 2.83117 ( 207) link_NAG-ASN : bond 0.00307 ( 51) link_NAG-ASN : angle 2.50643 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 285 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 85 GLU cc_start: 0.8286 (tp30) cc_final: 0.8008 (tp30) REVERT: 4 21 ILE cc_start: 0.5021 (OUTLIER) cc_final: 0.4733 (tt) REVERT: 7 1 GLU cc_start: 0.9062 (pt0) cc_final: 0.8238 (mt-10) REVERT: 7 33 MET cc_start: 0.8555 (tpp) cc_final: 0.8334 (tpp) REVERT: 7 60 ASP cc_start: 0.8658 (m-30) cc_final: 0.8373 (t0) REVERT: 8 28 ASN cc_start: 0.9255 (t0) cc_final: 0.8605 (t0) REVERT: 8 31 ASP cc_start: 0.8630 (m-30) cc_final: 0.7976 (m-30) REVERT: 8 43 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9077 (mmmm) REVERT: 8 80 MET cc_start: 0.8785 (tmm) cc_final: 0.8545 (tmm) REVERT: 8 100 ASP cc_start: 0.7402 (p0) cc_final: 0.6603 (t0) REVERT: C 95 MET cc_start: 0.8704 (ppp) cc_final: 0.8257 (ppp) REVERT: C 104 MET cc_start: 0.8934 (tmm) cc_final: 0.8350 (tmm) REVERT: C 425 ASN cc_start: 0.8705 (t0) cc_final: 0.8269 (t0) REVERT: D 530 MET cc_start: 0.7947 (ptp) cc_final: 0.7675 (ptp) REVERT: D 584 GLU cc_start: 0.8775 (tt0) cc_final: 0.8424 (tm-30) REVERT: D 652 GLN cc_start: 0.9327 (tt0) cc_final: 0.8696 (tp-100) REVERT: H 62 LYS cc_start: 0.9267 (tppt) cc_final: 0.9032 (ttpp) REVERT: H 66 LYS cc_start: 0.7401 (ptmt) cc_final: 0.6838 (tptp) REVERT: H 86 ASP cc_start: 0.8312 (m-30) cc_final: 0.7922 (m-30) REVERT: H 100 PHE cc_start: 0.7081 (m-80) cc_final: 0.6207 (m-80) REVERT: M 100 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7961 (mt-10) REVERT: M 100 MET cc_start: 0.8743 (mmm) cc_final: 0.8541 (mmm) REVERT: Q 1 GLN cc_start: 0.7361 (pp30) cc_final: 0.7145 (pp30) REVERT: Q 73 LEU cc_start: 0.8648 (mt) cc_final: 0.8409 (mt) REVERT: Q 76 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8309 (t0) REVERT: Q 80 MET cc_start: 0.8941 (tmm) cc_final: 0.8734 (tmm) REVERT: R 81 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8753 (tp30) REVERT: h 62 LYS cc_start: 0.9307 (tppt) cc_final: 0.8852 (ptmm) REVERT: h 86 ASP cc_start: 0.7429 (m-30) cc_final: 0.7104 (m-30) REVERT: h 94 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.6230 (ttp-110) REVERT: h 98 TYR cc_start: 0.8721 (m-80) cc_final: 0.7993 (m-80) REVERT: h 100 PHE cc_start: 0.6867 (m-80) cc_final: 0.6228 (m-80) REVERT: l 47 GLN cc_start: 0.7925 (mt0) cc_final: 0.7668 (mp10) REVERT: q 28 ASN cc_start: 0.9303 (t0) cc_final: 0.8659 (t0) REVERT: q 31 ASP cc_start: 0.8656 (m-30) cc_final: 0.8227 (m-30) REVERT: q 80 MET cc_start: 0.8861 (tmm) cc_final: 0.8543 (tmm) REVERT: r 1 GLU cc_start: 0.9087 (pt0) cc_final: 0.8499 (mt-10) REVERT: 2 95 MET cc_start: 0.8824 (ppp) cc_final: 0.8439 (ppp) REVERT: 2 104 MET cc_start: 0.8996 (tmm) cc_final: 0.8618 (tmm) REVERT: A 530 MET cc_start: 0.8078 (ptp) cc_final: 0.7792 (ptp) REVERT: A 584 GLU cc_start: 0.8724 (tt0) cc_final: 0.8453 (tm-30) REVERT: A 624 ASP cc_start: 0.8923 (p0) cc_final: 0.8492 (p0) REVERT: A 652 GLN cc_start: 0.9307 (tt0) cc_final: 0.8691 (tp-100) REVERT: c 577 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8794 (mp10) REVERT: c 584 GLU cc_start: 0.8691 (tt0) cc_final: 0.8341 (tm-30) REVERT: c 652 GLN cc_start: 0.9319 (tt0) cc_final: 0.8765 (tp-100) REVERT: c 654 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8913 (tm-30) REVERT: d 95 MET cc_start: 0.8729 (ppp) cc_final: 0.8275 (ppp) REVERT: d 100 MET cc_start: 0.9151 (ppp) cc_final: 0.8765 (ppp) REVERT: d 271 MET cc_start: 0.7953 (mmm) cc_final: 0.7733 (mmt) REVERT: d 434 MET cc_start: 0.9108 (ttm) cc_final: 0.8893 (ttp) outliers start: 71 outliers final: 37 residues processed: 339 average time/residue: 0.2166 time to fit residues: 116.5462 Evaluate side-chains 275 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 4 residue 21 ILE Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 98 CYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 31 ASP Chi-restraints excluded: chain Q residue 37 VAL Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain q residue 100 CYS Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 577 GLN Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 363 optimal weight: 6.9990 chunk 263 optimal weight: 0.0050 chunk 232 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 373 optimal weight: 4.9990 chunk 348 optimal weight: 0.8980 chunk 216 optimal weight: 10.0000 chunk 221 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 overall best weight: 1.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 577 GLN ** c 650 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 = 0.3417 r_free = 0.3417 target = 0.060951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.043681 restraints weight = 192055.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.044820 restraints weight = 104615.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045757 restraints weight = 74528.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046074 restraints weight = 60963.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.046395 restraints weight = 55275.701| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 33252 Z= 0.143 Angle : 0.731 15.855 45483 Z= 0.341 Chirality : 0.045 0.234 5442 Planarity : 0.004 0.056 5472 Dihedral : 9.998 81.747 7435 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.46 % Allowed : 11.32 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.71 (0.13), residues: 3777 helix: -0.32 (0.25), residues: 450 sheet: -0.71 (0.14), residues: 1290 loop : -1.61 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 94 TYR 0.021 0.001 TYR r 49 PHE 0.029 0.001 PHE Q 91 TRP 0.011 0.001 TRP Q 100F HIS 0.004 0.001 HIS 3 35 Details of bonding type rmsd covalent geometry : bond 0.00314 (33045) covalent geometry : angle 0.68417 (44907) SS BOND : bond 0.00483 ( 45) SS BOND : angle 2.14506 ( 90) hydrogen bonds : bond 0.03394 ( 1006) hydrogen bonds : angle 5.69443 ( 2712) link_ALPHA1-2 : bond 0.00421 ( 9) link_ALPHA1-2 : angle 1.91483 ( 27) link_ALPHA1-3 : bond 0.00892 ( 21) link_ALPHA1-3 : angle 1.91922 ( 63) link_ALPHA1-6 : bond 0.00710 ( 12) link_ALPHA1-6 : angle 1.68188 ( 36) link_BETA1-4 : bond 0.00649 ( 69) link_BETA1-4 : angle 2.78649 ( 207) link_NAG-ASN : bond 0.00314 ( 51) link_NAG-ASN : angle 2.28748 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 262 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9220 (tppt) cc_final: 0.8837 (ptmm) REVERT: 3 85 GLU cc_start: 0.8300 (tp30) cc_final: 0.8041 (tp30) REVERT: 5 41 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8235 (pp) REVERT: 7 1 GLU cc_start: 0.9053 (pt0) cc_final: 0.8227 (mt-10) REVERT: 7 60 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8441 (t0) REVERT: 8 28 ASN cc_start: 0.9243 (t0) cc_final: 0.8595 (t0) REVERT: 8 31 ASP cc_start: 0.8613 (m-30) cc_final: 0.7936 (m-30) REVERT: 8 43 LYS cc_start: 0.9376 (mmmm) cc_final: 0.9053 (mmmm) REVERT: 8 100 ASP cc_start: 0.7480 (p0) cc_final: 0.6607 (t0) REVERT: C 49 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: C 95 MET cc_start: 0.8883 (ppp) cc_final: 0.8331 (ppp) REVERT: C 271 MET cc_start: 0.8264 (mmm) cc_final: 0.7833 (mmt) REVERT: C 425 ASN cc_start: 0.8765 (t0) cc_final: 0.8377 (t0) REVERT: D 530 MET cc_start: 0.7966 (ptp) cc_final: 0.7724 (ptp) REVERT: D 584 GLU cc_start: 0.8809 (tt0) cc_final: 0.8423 (tm-30) REVERT: D 601 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7662 (ttpt) REVERT: D 652 GLN cc_start: 0.9291 (tt0) cc_final: 0.8769 (tp-100) REVERT: H 33 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: H 63 PHE cc_start: 0.7446 (m-80) cc_final: 0.6377 (m-80) REVERT: H 66 LYS cc_start: 0.7406 (ptmt) cc_final: 0.6844 (tptp) REVERT: H 86 ASP cc_start: 0.8372 (m-30) cc_final: 0.7947 (m-30) REVERT: H 100 PHE cc_start: 0.7078 (m-80) cc_final: 0.6201 (m-80) REVERT: L 108 LYS cc_start: 0.7217 (mmtt) cc_final: 0.6666 (tppt) REVERT: M 100 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7900 (mt-10) REVERT: Q 3 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8323 (mm-40) REVERT: Q 76 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8075 (t0) REVERT: Q 80 MET cc_start: 0.8911 (tmm) cc_final: 0.8709 (tmm) REVERT: Q 100 ASP cc_start: 0.7268 (p0) cc_final: 0.5971 (t0) REVERT: R 60 ASP cc_start: 0.8887 (t70) cc_final: 0.8567 (t0) REVERT: R 81 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8725 (tp30) REVERT: h 62 LYS cc_start: 0.9353 (tppt) cc_final: 0.8928 (ptmm) REVERT: h 86 ASP cc_start: 0.7501 (m-30) cc_final: 0.7151 (m-30) REVERT: h 94 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6375 (ttp-110) REVERT: h 98 TYR cc_start: 0.8748 (m-80) cc_final: 0.8319 (m-80) REVERT: h 100 PHE cc_start: 0.6984 (m-80) cc_final: 0.6325 (m-80) REVERT: l 47 GLN cc_start: 0.8020 (mt0) cc_final: 0.7796 (mp10) REVERT: q 1 GLN cc_start: 0.7729 (pp30) cc_final: 0.7493 (pp30) REVERT: q 3 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8519 (mm-40) REVERT: q 28 ASN cc_start: 0.9278 (t0) cc_final: 0.8617 (t0) REVERT: q 31 ASP cc_start: 0.8673 (m-30) cc_final: 0.8232 (m-30) REVERT: q 99 ASP cc_start: 0.8484 (p0) cc_final: 0.8275 (p0) REVERT: r 1 GLU cc_start: 0.9088 (pt0) cc_final: 0.8444 (mt-10) REVERT: 2 95 MET cc_start: 0.8966 (ppp) cc_final: 0.8452 (ppp) REVERT: 2 104 MET cc_start: 0.9040 (tmm) cc_final: 0.8780 (tmm) REVERT: 2 271 MET cc_start: 0.8349 (mmm) cc_final: 0.7817 (mmt) REVERT: A 530 MET cc_start: 0.8113 (ptp) cc_final: 0.7816 (ptp) REVERT: A 584 GLU cc_start: 0.8737 (tt0) cc_final: 0.8468 (tm-30) REVERT: A 652 GLN cc_start: 0.9317 (tt0) cc_final: 0.8720 (tp-100) REVERT: c 584 GLU cc_start: 0.8715 (tt0) cc_final: 0.8374 (tm-30) REVERT: c 652 GLN cc_start: 0.9316 (tt0) cc_final: 0.8778 (tp-100) REVERT: d 95 MET cc_start: 0.8848 (ppp) cc_final: 0.8250 (ppp) REVERT: d 100 MET cc_start: 0.9126 (ppp) cc_final: 0.8815 (ppp) REVERT: d 161 MET cc_start: 0.9505 (tpt) cc_final: 0.9196 (tpp) REVERT: d 434 MET cc_start: 0.9131 (ttm) cc_final: 0.8880 (ttp) outliers start: 82 outliers final: 48 residues processed: 330 average time/residue: 0.2102 time to fit residues: 111.2864 Evaluate side-chains 281 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 226 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 95 LEU Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 51 THR Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain 2 residue 496 VAL Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 577 GLN Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 200 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 287 optimal weight: 10.0000 chunk 95 optimal weight: 0.0060 chunk 171 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 354 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 95CASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 ASN h 3 GLN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 543 ASN c 577 GLN ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.043406 restraints weight = 194197.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.044513 restraints weight = 105753.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.045166 restraints weight = 75539.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045831 restraints weight = 62996.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.045989 restraints weight = 55766.799| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33252 Z= 0.156 Angle : 0.709 15.749 45483 Z= 0.329 Chirality : 0.045 0.238 5442 Planarity : 0.004 0.054 5472 Dihedral : 9.363 80.830 7435 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.97 % Allowed : 11.62 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.61 (0.13), residues: 3777 helix: -0.26 (0.25), residues: 450 sheet: -0.67 (0.14), residues: 1287 loop : -1.52 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 30 TYR 0.019 0.001 TYR 3 79 PHE 0.023 0.001 PHE Q 91 TRP 0.027 0.001 TRP Q 100F HIS 0.004 0.001 HIS 2 374 Details of bonding type rmsd covalent geometry : bond 0.00339 (33045) covalent geometry : angle 0.66549 (44907) SS BOND : bond 0.00491 ( 45) SS BOND : angle 1.49620 ( 90) hydrogen bonds : bond 0.03421 ( 1006) hydrogen bonds : angle 5.63095 ( 2712) link_ALPHA1-2 : bond 0.00356 ( 9) link_ALPHA1-2 : angle 1.91329 ( 27) link_ALPHA1-3 : bond 0.00827 ( 21) link_ALPHA1-3 : angle 1.98708 ( 63) link_ALPHA1-6 : bond 0.00809 ( 12) link_ALPHA1-6 : angle 1.73070 ( 36) link_BETA1-4 : bond 0.00572 ( 69) link_BETA1-4 : angle 2.76551 ( 207) link_NAG-ASN : bond 0.00349 ( 51) link_NAG-ASN : angle 2.21301 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 246 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9227 (tppt) cc_final: 0.8814 (ptmm) REVERT: 3 82 ARG cc_start: 0.8115 (mpp80) cc_final: 0.7774 (mpp-170) REVERT: 5 41 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8258 (pp) REVERT: 7 1 GLU cc_start: 0.9093 (pt0) cc_final: 0.8218 (mt-10) REVERT: 7 60 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8423 (t0) REVERT: 8 28 ASN cc_start: 0.9302 (t0) cc_final: 0.8636 (t0) REVERT: 8 31 ASP cc_start: 0.8619 (m-30) cc_final: 0.7926 (m-30) REVERT: 8 43 LYS cc_start: 0.9386 (mmmm) cc_final: 0.8987 (mmmm) REVERT: 8 100 ASP cc_start: 0.7414 (p0) cc_final: 0.6489 (t0) REVERT: C 49 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7946 (mm-30) REVERT: C 95 MET cc_start: 0.8997 (ppp) cc_final: 0.8271 (ppp) REVERT: C 425 ASN cc_start: 0.8777 (t0) cc_final: 0.8417 (t0) REVERT: D 530 MET cc_start: 0.7993 (ptp) cc_final: 0.7705 (ptp) REVERT: D 584 GLU cc_start: 0.8833 (tt0) cc_final: 0.8447 (tm-30) REVERT: D 601 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7708 (ttpt) REVERT: H 62 LYS cc_start: 0.9277 (tppt) cc_final: 0.9047 (ttpp) REVERT: H 66 LYS cc_start: 0.7690 (ptmt) cc_final: 0.7144 (tptp) REVERT: H 86 ASP cc_start: 0.8334 (m-30) cc_final: 0.7834 (m-30) REVERT: H 100 PHE cc_start: 0.7136 (m-80) cc_final: 0.6373 (m-80) REVERT: L 108 LYS cc_start: 0.6978 (mmtt) cc_final: 0.6284 (tppt) REVERT: M 100 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7883 (mt-10) REVERT: Q 76 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.7950 (t0) REVERT: R 60 ASP cc_start: 0.8909 (t70) cc_final: 0.8594 (t0) REVERT: R 77 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8827 (ttpp) REVERT: h 86 ASP cc_start: 0.7555 (m-30) cc_final: 0.7150 (m-30) REVERT: h 94 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.6336 (ttp-110) REVERT: h 98 TYR cc_start: 0.8777 (m-80) cc_final: 0.8346 (m-80) REVERT: h 100 PHE cc_start: 0.6999 (m-80) cc_final: 0.6332 (m-80) REVERT: l 47 GLN cc_start: 0.8021 (mt0) cc_final: 0.7785 (mp10) REVERT: l 98 HIS cc_start: 0.7590 (m90) cc_final: 0.7369 (m90) REVERT: q 28 ASN cc_start: 0.9290 (t0) cc_final: 0.8636 (t0) REVERT: q 31 ASP cc_start: 0.8658 (m-30) cc_final: 0.8207 (m-30) REVERT: q 100 ASP cc_start: 0.7513 (p0) cc_final: 0.6322 (t0) REVERT: r 1 GLU cc_start: 0.9061 (pt0) cc_final: 0.8429 (mt-10) REVERT: 2 95 MET cc_start: 0.9062 (ppp) cc_final: 0.8430 (ppp) REVERT: 2 271 MET cc_start: 0.8434 (mmm) cc_final: 0.7942 (mmt) REVERT: A 530 MET cc_start: 0.8188 (ptp) cc_final: 0.7907 (ptp) REVERT: A 584 GLU cc_start: 0.8740 (tt0) cc_final: 0.8483 (tm-30) REVERT: A 621 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: A 652 GLN cc_start: 0.9323 (tt0) cc_final: 0.8730 (tp-100) REVERT: c 530 MET cc_start: 0.7830 (ptp) cc_final: 0.7070 (mpp) REVERT: c 584 GLU cc_start: 0.8707 (tt0) cc_final: 0.8361 (tm-30) REVERT: c 601 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7735 (ttpt) REVERT: c 624 ASP cc_start: 0.9035 (p0) cc_final: 0.8686 (p0) REVERT: d 95 MET cc_start: 0.8987 (ppp) cc_final: 0.8314 (ppp) REVERT: d 100 MET cc_start: 0.9121 (ppp) cc_final: 0.8840 (ppp) REVERT: d 161 MET cc_start: 0.9515 (tpt) cc_final: 0.9213 (tpp) REVERT: d 271 MET cc_start: 0.7820 (mmt) cc_final: 0.7549 (mmm) REVERT: d 434 MET cc_start: 0.9103 (ttm) cc_final: 0.8888 (ttp) outliers start: 99 outliers final: 62 residues processed: 327 average time/residue: 0.2141 time to fit residues: 112.2010 Evaluate side-chains 299 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 229 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 25 SER Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 51 THR Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 98 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 630 GLN Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain d residue 496 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 127 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 12 optimal weight: 50.0000 chunk 264 optimal weight: 1.9990 chunk 266 optimal weight: 2.9990 chunk 259 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 265 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 32 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 35 ASN m 32 ASN q 3 GLN 2 302 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 577 GLN c 630 GLN ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.059520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.042693 restraints weight = 198248.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.043720 restraints weight = 107037.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044334 restraints weight = 76038.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.044792 restraints weight = 63118.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045082 restraints weight = 57007.375| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 33252 Z= 0.236 Angle : 0.767 15.825 45483 Z= 0.355 Chirality : 0.046 0.254 5442 Planarity : 0.004 0.054 5472 Dihedral : 9.180 80.586 7435 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.88 % Allowed : 11.95 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.13), residues: 3777 helix: -0.38 (0.25), residues: 450 sheet: -0.76 (0.14), residues: 1278 loop : -1.44 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 8 61 TYR 0.014 0.001 TYR d 318 PHE 0.022 0.002 PHE Q 91 TRP 0.022 0.002 TRP 2 427 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00513 (33045) covalent geometry : angle 0.72397 (44907) SS BOND : bond 0.00323 ( 45) SS BOND : angle 1.47617 ( 90) hydrogen bonds : bond 0.03660 ( 1006) hydrogen bonds : angle 5.79265 ( 2712) link_ALPHA1-2 : bond 0.00347 ( 9) link_ALPHA1-2 : angle 1.97672 ( 27) link_ALPHA1-3 : bond 0.00692 ( 21) link_ALPHA1-3 : angle 2.10633 ( 63) link_ALPHA1-6 : bond 0.00801 ( 12) link_ALPHA1-6 : angle 1.81254 ( 36) link_BETA1-4 : bond 0.00541 ( 69) link_BETA1-4 : angle 2.82030 ( 207) link_NAG-ASN : bond 0.00577 ( 51) link_NAG-ASN : angle 2.41990 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 242 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9195 (tppt) cc_final: 0.8796 (ptmm) REVERT: 5 41 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8152 (pp) REVERT: 7 1 GLU cc_start: 0.9198 (pt0) cc_final: 0.8146 (mt-10) REVERT: 7 60 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8411 (t0) REVERT: 7 77 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8652 (ttpp) REVERT: 8 28 ASN cc_start: 0.9337 (t0) cc_final: 0.8669 (t0) REVERT: 8 31 ASP cc_start: 0.8687 (m-30) cc_final: 0.7959 (m-30) REVERT: 8 43 LYS cc_start: 0.9372 (mmmm) cc_final: 0.8982 (mmmm) REVERT: 8 80 MET cc_start: 0.8721 (tmm) cc_final: 0.8469 (tmm) REVERT: 8 100 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.6654 (t0) REVERT: C 49 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: C 95 MET cc_start: 0.9146 (ppp) cc_final: 0.8327 (ppp) REVERT: C 271 MET cc_start: 0.8309 (mmm) cc_final: 0.7829 (mmt) REVERT: C 425 ASN cc_start: 0.8581 (t0) cc_final: 0.8247 (t0) REVERT: D 530 MET cc_start: 0.8087 (ptp) cc_final: 0.7804 (ptp) REVERT: D 584 GLU cc_start: 0.8861 (tt0) cc_final: 0.8489 (tm-30) REVERT: D 601 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7729 (ttpt) REVERT: D 624 ASP cc_start: 0.9047 (p0) cc_final: 0.8741 (p0) REVERT: D 626 MET cc_start: 0.8866 (tpp) cc_final: 0.8464 (tpp) REVERT: H 63 PHE cc_start: 0.7592 (m-80) cc_final: 0.6586 (m-80) REVERT: H 66 LYS cc_start: 0.7802 (ptmt) cc_final: 0.7186 (tptp) REVERT: H 86 ASP cc_start: 0.8333 (m-30) cc_final: 0.7875 (m-30) REVERT: H 100 PHE cc_start: 0.7301 (m-80) cc_final: 0.6613 (m-80) REVERT: M 100 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7873 (mt-10) REVERT: Q 76 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8056 (t0) REVERT: Q 100 ASP cc_start: 0.7244 (p0) cc_final: 0.6120 (t0) REVERT: R 77 LYS cc_start: 0.9174 (ttpp) cc_final: 0.8909 (ttpp) REVERT: h 62 LYS cc_start: 0.9203 (tppt) cc_final: 0.8825 (ptmm) REVERT: h 86 ASP cc_start: 0.7607 (m-30) cc_final: 0.7235 (m-30) REVERT: h 94 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.6268 (ttp-110) REVERT: h 100 PHE cc_start: 0.7197 (m-80) cc_final: 0.6527 (m-80) REVERT: l 2 PHE cc_start: 0.7144 (m-80) cc_final: 0.6885 (m-80) REVERT: l 47 GLN cc_start: 0.8024 (mt0) cc_final: 0.7807 (mp10) REVERT: q 28 ASN cc_start: 0.9324 (t0) cc_final: 0.8757 (t0) REVERT: q 31 ASP cc_start: 0.8688 (m-30) cc_final: 0.7894 (m-30) REVERT: q 100 ASP cc_start: 0.7550 (p0) cc_final: 0.6446 (t0) REVERT: r 1 GLU cc_start: 0.9083 (pt0) cc_final: 0.8372 (mt-10) REVERT: 2 95 MET cc_start: 0.9225 (ppp) cc_final: 0.8542 (ppp) REVERT: 2 104 MET cc_start: 0.8937 (tmm) cc_final: 0.8297 (tmm) REVERT: 2 125 LEU cc_start: 0.9567 (tt) cc_final: 0.9276 (tt) REVERT: 2 271 MET cc_start: 0.8450 (mmm) cc_final: 0.7989 (mmt) REVERT: A 530 MET cc_start: 0.8208 (ptp) cc_final: 0.7926 (ptp) REVERT: A 584 GLU cc_start: 0.8777 (tt0) cc_final: 0.8488 (tm-30) REVERT: A 621 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8545 (tm-30) REVERT: A 652 GLN cc_start: 0.9332 (tt0) cc_final: 0.8757 (tp-100) REVERT: c 530 MET cc_start: 0.8000 (ptp) cc_final: 0.7104 (mpp) REVERT: c 584 GLU cc_start: 0.8730 (tt0) cc_final: 0.8390 (tm-30) REVERT: c 626 MET cc_start: 0.8496 (tpp) cc_final: 0.7590 (tpp) REVERT: c 630 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8879 (pt0) REVERT: d 95 MET cc_start: 0.9148 (ppp) cc_final: 0.8409 (ppp) REVERT: d 100 MET cc_start: 0.9155 (ppp) cc_final: 0.8933 (ppp) REVERT: d 125 LEU cc_start: 0.9472 (tt) cc_final: 0.9256 (tt) REVERT: d 161 MET cc_start: 0.9516 (tpt) cc_final: 0.9244 (tpp) REVERT: d 271 MET cc_start: 0.7967 (mmt) cc_final: 0.7578 (mmm) REVERT: d 434 MET cc_start: 0.9139 (ttm) cc_final: 0.8889 (ttp) outliers start: 96 outliers final: 68 residues processed: 320 average time/residue: 0.2170 time to fit residues: 111.3059 Evaluate side-chains 303 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 226 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 5 residue 41 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 51 THR Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 98 CYS Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain l residue 35 ASN Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 100 MET Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 595 ILE Chi-restraints excluded: chain c residue 630 GLN Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain d residue 496 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 212 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 348 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 362 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 313 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 23 ASN A 630 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 630 GLN ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.058641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.041651 restraints weight = 200195.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.042664 restraints weight = 109227.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043137 restraints weight = 78383.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.043725 restraints weight = 67186.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.043974 restraints weight = 60140.527| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 33252 Z= 0.282 Angle : 0.808 15.016 45483 Z= 0.378 Chirality : 0.047 0.266 5442 Planarity : 0.004 0.051 5472 Dihedral : 9.157 81.003 7435 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.09 % Allowed : 12.13 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.13), residues: 3777 helix: -0.53 (0.25), residues: 450 sheet: -0.90 (0.14), residues: 1266 loop : -1.43 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 94 TYR 0.017 0.002 TYR l 37 PHE 0.022 0.002 PHE Q 91 TRP 0.027 0.002 TRP C 427 HIS 0.006 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00610 (33045) covalent geometry : angle 0.76573 (44907) SS BOND : bond 0.00296 ( 45) SS BOND : angle 1.50869 ( 90) hydrogen bonds : bond 0.03850 ( 1006) hydrogen bonds : angle 5.97230 ( 2712) link_ALPHA1-2 : bond 0.00402 ( 9) link_ALPHA1-2 : angle 2.05157 ( 27) link_ALPHA1-3 : bond 0.00649 ( 21) link_ALPHA1-3 : angle 2.17067 ( 63) link_ALPHA1-6 : bond 0.00807 ( 12) link_ALPHA1-6 : angle 1.86364 ( 36) link_BETA1-4 : bond 0.00554 ( 69) link_BETA1-4 : angle 2.83964 ( 207) link_NAG-ASN : bond 0.00680 ( 51) link_NAG-ASN : angle 2.53873 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 236 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9157 (tppt) cc_final: 0.8782 (ptmm) REVERT: 7 60 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8339 (t0) REVERT: 7 77 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8691 (ttpp) REVERT: 8 28 ASN cc_start: 0.9362 (t0) cc_final: 0.8957 (t0) REVERT: 8 43 LYS cc_start: 0.9355 (mmmm) cc_final: 0.8968 (mmmm) REVERT: 8 80 MET cc_start: 0.8641 (tmm) cc_final: 0.8399 (tmm) REVERT: 8 100 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.6826 (t0) REVERT: C 49 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: C 95 MET cc_start: 0.9198 (ppp) cc_final: 0.8365 (ppp) REVERT: C 271 MET cc_start: 0.8359 (mmm) cc_final: 0.7902 (mmt) REVERT: C 425 ASN cc_start: 0.8663 (t0) cc_final: 0.8351 (t0) REVERT: D 530 MET cc_start: 0.8033 (ptp) cc_final: 0.7760 (ptp) REVERT: D 584 GLU cc_start: 0.8830 (tt0) cc_final: 0.8464 (tm-30) REVERT: D 601 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7864 (ttpt) REVERT: D 626 MET cc_start: 0.8816 (tpp) cc_final: 0.8404 (tpp) REVERT: H 33 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: H 63 PHE cc_start: 0.7549 (m-80) cc_final: 0.6564 (m-80) REVERT: H 66 LYS cc_start: 0.7909 (ptmt) cc_final: 0.7419 (tptp) REVERT: H 86 ASP cc_start: 0.8278 (m-30) cc_final: 0.7844 (m-30) REVERT: H 100 PHE cc_start: 0.7272 (m-80) cc_final: 0.6537 (m-80) REVERT: Q 76 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8113 (t0) REVERT: Q 100 ASP cc_start: 0.7287 (p0) cc_final: 0.6283 (t0) REVERT: h 62 LYS cc_start: 0.9204 (tppt) cc_final: 0.8801 (ptmm) REVERT: h 86 ASP cc_start: 0.7585 (m-30) cc_final: 0.7216 (m-30) REVERT: h 94 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.6197 (ttp-110) REVERT: h 100 PHE cc_start: 0.7236 (m-80) cc_final: 0.6580 (m-80) REVERT: m 77 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7732 (tt) REVERT: q 28 ASN cc_start: 0.9387 (t0) cc_final: 0.8650 (t0) REVERT: q 31 ASP cc_start: 0.8707 (m-30) cc_final: 0.8062 (m-30) REVERT: q 100 ASP cc_start: 0.7666 (p0) cc_final: 0.6502 (t0) REVERT: r 1 GLU cc_start: 0.9089 (pt0) cc_final: 0.8343 (mt-10) REVERT: r 24 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8714 (ttmm) REVERT: 2 95 MET cc_start: 0.9253 (ppp) cc_final: 0.8541 (ppp) REVERT: 2 125 LEU cc_start: 0.9573 (tt) cc_final: 0.9282 (tt) REVERT: 2 271 MET cc_start: 0.8442 (mmm) cc_final: 0.8009 (mmt) REVERT: A 530 MET cc_start: 0.8247 (ptp) cc_final: 0.7959 (ptp) REVERT: A 584 GLU cc_start: 0.8789 (tt0) cc_final: 0.8522 (tm-30) REVERT: c 530 MET cc_start: 0.8009 (ptp) cc_final: 0.7092 (mpp) REVERT: c 584 GLU cc_start: 0.8712 (tt0) cc_final: 0.8386 (tm-30) REVERT: c 601 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7985 (ttpt) REVERT: d 95 MET cc_start: 0.9232 (ppp) cc_final: 0.8477 (ppp) REVERT: d 100 MET cc_start: 0.9150 (ppp) cc_final: 0.8944 (ppp) REVERT: d 125 LEU cc_start: 0.9443 (tt) cc_final: 0.9150 (tt) REVERT: d 161 MET cc_start: 0.9506 (tpt) cc_final: 0.9280 (tpp) REVERT: d 271 MET cc_start: 0.8034 (mmt) cc_final: 0.7618 (mmm) REVERT: d 434 MET cc_start: 0.9075 (ttm) cc_final: 0.8862 (ttp) outliers start: 103 outliers final: 69 residues processed: 320 average time/residue: 0.2092 time to fit residues: 107.5265 Evaluate side-chains 298 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 219 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 6 residue 90 ILE Chi-restraints excluded: chain 7 residue 51 THR Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 60 ASP Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 98 CYS Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain h residue 94 ARG Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 90 ILE Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 53 PHE Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 100 MET Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 539 VAL Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 595 ILE Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain c residue 608 VAL Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain d residue 374 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 360 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 347 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 35 ASN m 23 ASN ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 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 = 0.3387 r_free = 0.3387 target = 0.059877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.042881 restraints weight = 195540.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.043940 restraints weight = 106418.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.044566 restraints weight = 76123.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.045220 restraints weight = 63567.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.045458 restraints weight = 56305.589| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33252 Z= 0.154 Angle : 0.735 15.873 45483 Z= 0.342 Chirality : 0.046 0.267 5442 Planarity : 0.004 0.058 5472 Dihedral : 8.737 79.229 7435 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.34 % Allowed : 13.09 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.52 (0.14), residues: 3777 helix: -0.38 (0.25), residues: 447 sheet: -0.64 (0.14), residues: 1269 loop : -1.38 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 94 TYR 0.017 0.001 TYR L 91 PHE 0.021 0.001 PHE Q 91 TRP 0.023 0.001 TRP C 427 HIS 0.005 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00338 (33045) covalent geometry : angle 0.69455 (44907) SS BOND : bond 0.00241 ( 45) SS BOND : angle 1.48841 ( 90) hydrogen bonds : bond 0.03573 ( 1006) hydrogen bonds : angle 5.75565 ( 2712) link_ALPHA1-2 : bond 0.00340 ( 9) link_ALPHA1-2 : angle 1.96437 ( 27) link_ALPHA1-3 : bond 0.00774 ( 21) link_ALPHA1-3 : angle 1.81857 ( 63) link_ALPHA1-6 : bond 0.00816 ( 12) link_ALPHA1-6 : angle 1.73262 ( 36) link_BETA1-4 : bond 0.00558 ( 69) link_BETA1-4 : angle 2.75166 ( 207) link_NAG-ASN : bond 0.00352 ( 51) link_NAG-ASN : angle 2.15686 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 248 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9191 (tppt) cc_final: 0.8798 (ptmm) REVERT: 7 60 ASP cc_start: 0.8666 (m-30) cc_final: 0.8385 (t0) REVERT: 7 77 LYS cc_start: 0.9008 (ttpp) cc_final: 0.8658 (ttpp) REVERT: 8 28 ASN cc_start: 0.9346 (t0) cc_final: 0.8752 (t0) REVERT: 8 31 ASP cc_start: 0.8723 (m-30) cc_final: 0.8097 (m-30) REVERT: 8 43 LYS cc_start: 0.9361 (mmmm) cc_final: 0.8985 (mmmm) REVERT: 8 100 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6852 (t0) REVERT: C 49 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7976 (mm-30) REVERT: C 95 MET cc_start: 0.9205 (ppp) cc_final: 0.8298 (ppp) REVERT: C 271 MET cc_start: 0.8310 (mmm) cc_final: 0.7868 (mmt) REVERT: C 425 ASN cc_start: 0.8539 (t0) cc_final: 0.8331 (t0) REVERT: C 426 MET cc_start: 0.8596 (ppp) cc_final: 0.8207 (ppp) REVERT: D 530 MET cc_start: 0.7983 (ptp) cc_final: 0.7707 (ptp) REVERT: D 584 GLU cc_start: 0.8852 (tt0) cc_final: 0.8428 (tm-30) REVERT: D 601 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7779 (ttpt) REVERT: D 626 MET cc_start: 0.8776 (tpp) cc_final: 0.8537 (tpp) REVERT: H 33 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: H 63 PHE cc_start: 0.7664 (m-80) cc_final: 0.6689 (m-80) REVERT: H 66 LYS cc_start: 0.7776 (ptmt) cc_final: 0.7302 (tptp) REVERT: H 86 ASP cc_start: 0.8265 (m-30) cc_final: 0.7807 (m-30) REVERT: H 100 PHE cc_start: 0.7215 (m-80) cc_final: 0.6381 (m-80) REVERT: M 100 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7850 (mt-10) REVERT: Q 76 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.7973 (t0) REVERT: Q 100 ASP cc_start: 0.7299 (p0) cc_final: 0.6515 (t0) REVERT: h 62 LYS cc_start: 0.9289 (tppt) cc_final: 0.8887 (ptmm) REVERT: h 86 ASP cc_start: 0.7553 (m-30) cc_final: 0.7155 (m-30) REVERT: h 98 TYR cc_start: 0.8771 (m-80) cc_final: 0.8259 (m-80) REVERT: l 47 GLN cc_start: 0.8078 (mt0) cc_final: 0.7833 (mp10) REVERT: m 77 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7904 (tt) REVERT: q 28 ASN cc_start: 0.9414 (t0) cc_final: 0.8721 (t0) REVERT: q 31 ASP cc_start: 0.8687 (m-30) cc_final: 0.8085 (m-30) REVERT: q 100 ASP cc_start: 0.7554 (p0) cc_final: 0.6564 (t0) REVERT: r 1 GLU cc_start: 0.9075 (pt0) cc_final: 0.8318 (mt-10) REVERT: 2 95 MET cc_start: 0.9257 (ppp) cc_final: 0.8424 (ppp) REVERT: 2 125 LEU cc_start: 0.9537 (tt) cc_final: 0.9333 (tt) REVERT: 2 271 MET cc_start: 0.8510 (mmm) cc_final: 0.8138 (mmt) REVERT: A 530 MET cc_start: 0.8198 (ptp) cc_final: 0.7893 (ptp) REVERT: A 584 GLU cc_start: 0.8782 (tt0) cc_final: 0.8469 (tm-30) REVERT: c 584 GLU cc_start: 0.8699 (tt0) cc_final: 0.8316 (tm-30) REVERT: c 601 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7963 (ttpt) REVERT: d 95 MET cc_start: 0.9226 (ppp) cc_final: 0.8386 (ppp) REVERT: d 100 MET cc_start: 0.9143 (ppp) cc_final: 0.8941 (ppp) REVERT: d 125 LEU cc_start: 0.9429 (tt) cc_final: 0.9161 (tt) REVERT: d 161 MET cc_start: 0.9527 (tpt) cc_final: 0.9236 (tpp) REVERT: d 271 MET cc_start: 0.7918 (mmt) cc_final: 0.7523 (mmm) REVERT: d 434 MET cc_start: 0.9002 (ttm) cc_final: 0.8748 (ttp) outliers start: 78 outliers final: 58 residues processed: 310 average time/residue: 0.2165 time to fit residues: 107.5880 Evaluate side-chains 292 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 51 THR Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 98 CYS Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain Q residue 98 CYS Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 35 ASN Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 100 MET Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 573 ILE Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 PHE Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 224 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 344 optimal weight: 0.0060 chunk 325 optimal weight: 10.0000 chunk 345 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 ASN ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 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 = 0.3397 r_free = 0.3397 target = 0.060343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043319 restraints weight = 193439.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.044402 restraints weight = 105374.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.045083 restraints weight = 75027.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.045482 restraints weight = 61788.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045791 restraints weight = 55719.902| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33252 Z= 0.131 Angle : 0.728 15.713 45483 Z= 0.338 Chirality : 0.046 0.262 5442 Planarity : 0.004 0.055 5472 Dihedral : 8.421 77.616 7435 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.92 % Allowed : 13.87 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.41 (0.14), residues: 3777 helix: -0.41 (0.25), residues: 447 sheet: -0.56 (0.14), residues: 1305 loop : -1.29 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 94 TYR 0.014 0.001 TYR L 91 PHE 0.021 0.001 PHE Q 91 TRP 0.034 0.001 TRP d 427 HIS 0.004 0.001 HIS 3 35 Details of bonding type rmsd covalent geometry : bond 0.00289 (33045) covalent geometry : angle 0.68937 (44907) SS BOND : bond 0.00228 ( 45) SS BOND : angle 1.50721 ( 90) hydrogen bonds : bond 0.03465 ( 1006) hydrogen bonds : angle 5.63447 ( 2712) link_ALPHA1-2 : bond 0.00326 ( 9) link_ALPHA1-2 : angle 1.89792 ( 27) link_ALPHA1-3 : bond 0.00806 ( 21) link_ALPHA1-3 : angle 1.71767 ( 63) link_ALPHA1-6 : bond 0.00849 ( 12) link_ALPHA1-6 : angle 1.70839 ( 36) link_BETA1-4 : bond 0.00558 ( 69) link_BETA1-4 : angle 2.72281 ( 207) link_NAG-ASN : bond 0.00291 ( 51) link_NAG-ASN : angle 2.01704 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7554 Ramachandran restraints generated. 3777 Oldfield, 0 Emsley, 3777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 241 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 62 LYS cc_start: 0.9192 (tppt) cc_final: 0.8816 (ptmm) REVERT: 7 60 ASP cc_start: 0.8663 (m-30) cc_final: 0.8420 (t0) REVERT: 7 77 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8631 (ttpp) REVERT: 8 28 ASN cc_start: 0.9351 (t0) cc_final: 0.8758 (t0) REVERT: 8 31 ASP cc_start: 0.8756 (m-30) cc_final: 0.8170 (m-30) REVERT: 8 43 LYS cc_start: 0.9332 (mmmm) cc_final: 0.8978 (mmmm) REVERT: 8 100 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.6767 (t0) REVERT: C 95 MET cc_start: 0.9197 (ppp) cc_final: 0.8249 (ppp) REVERT: C 104 MET cc_start: 0.8815 (tmm) cc_final: 0.8244 (tmm) REVERT: C 271 MET cc_start: 0.8313 (mmm) cc_final: 0.7864 (mmt) REVERT: D 530 MET cc_start: 0.7938 (ptp) cc_final: 0.7664 (ptp) REVERT: D 584 GLU cc_start: 0.8900 (tt0) cc_final: 0.8401 (tm-30) REVERT: D 601 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7787 (ttpt) REVERT: D 626 MET cc_start: 0.8753 (tpp) cc_final: 0.8466 (tpp) REVERT: H 33 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: H 63 PHE cc_start: 0.7772 (m-80) cc_final: 0.6821 (m-80) REVERT: H 66 LYS cc_start: 0.7772 (ptmt) cc_final: 0.7304 (tptp) REVERT: H 86 ASP cc_start: 0.8268 (m-30) cc_final: 0.7778 (m-30) REVERT: H 100 PHE cc_start: 0.7075 (m-80) cc_final: 0.6243 (m-80) REVERT: L 2 PHE cc_start: 0.7617 (m-80) cc_final: 0.7386 (m-80) REVERT: L 108 LYS cc_start: 0.7458 (mmtt) cc_final: 0.6952 (tppt) REVERT: Q 76 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.7979 (t0) REVERT: Q 100 ASP cc_start: 0.7125 (p0) cc_final: 0.6313 (t0) REVERT: h 62 LYS cc_start: 0.9307 (tppt) cc_final: 0.8915 (ptmm) REVERT: h 86 ASP cc_start: 0.7550 (m-30) cc_final: 0.7161 (m-30) REVERT: h 98 TYR cc_start: 0.8791 (m-80) cc_final: 0.8345 (m-80) REVERT: h 100 PHE cc_start: 0.7203 (m-80) cc_final: 0.6522 (m-80) REVERT: m 77 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7826 (tt) REVERT: q 28 ASN cc_start: 0.9405 (t0) cc_final: 0.8679 (t0) REVERT: q 31 ASP cc_start: 0.8677 (m-30) cc_final: 0.8044 (m-30) REVERT: q 100 ASP cc_start: 0.7527 (p0) cc_final: 0.6557 (t0) REVERT: r 1 GLU cc_start: 0.9101 (pt0) cc_final: 0.8350 (mt-10) REVERT: 2 95 MET cc_start: 0.9260 (ppp) cc_final: 0.8413 (ppp) REVERT: 2 125 LEU cc_start: 0.9512 (tt) cc_final: 0.9273 (tt) REVERT: 2 271 MET cc_start: 0.8536 (mmm) cc_final: 0.8171 (mmt) REVERT: A 530 MET cc_start: 0.8137 (ptp) cc_final: 0.7804 (ptp) REVERT: A 584 GLU cc_start: 0.8832 (tt0) cc_final: 0.8484 (tm-30) REVERT: A 652 GLN cc_start: 0.9308 (tt0) cc_final: 0.9046 (pp30) REVERT: c 530 MET cc_start: 0.7887 (ptp) cc_final: 0.7165 (mpp) REVERT: c 584 GLU cc_start: 0.8723 (tt0) cc_final: 0.8334 (tm-30) REVERT: c 601 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7847 (ttpt) REVERT: d 95 MET cc_start: 0.9174 (ppp) cc_final: 0.8272 (ppp) REVERT: d 125 LEU cc_start: 0.9400 (tt) cc_final: 0.9130 (tt) REVERT: d 161 MET cc_start: 0.9537 (tpt) cc_final: 0.9208 (tpp) REVERT: d 271 MET cc_start: 0.7937 (mmt) cc_final: 0.7382 (mmm) outliers start: 64 outliers final: 53 residues processed: 292 average time/residue: 0.2080 time to fit residues: 97.6223 Evaluate side-chains 288 residues out of total 3330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 229 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 42 VAL Chi-restraints excluded: chain 3 residue 98 TYR Chi-restraints excluded: chain 4 residue 52 LEU Chi-restraints excluded: chain 5 residue 109 VAL Chi-restraints excluded: chain 7 residue 51 THR Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 7 residue 78 LEU Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 98 CYS Chi-restraints excluded: chain 8 residue 100 CYS Chi-restraints excluded: chain 8 residue 100 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 601 LYS Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 76 ASP Chi-restraints excluded: chain R residue 56 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain h residue 42 VAL Chi-restraints excluded: chain l residue 3 LEU Chi-restraints excluded: chain l residue 52 LEU Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain r residue 34 THR Chi-restraints excluded: chain r residue 51 THR Chi-restraints excluded: chain r residue 56 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 100 MET Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 292 VAL Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 423 ILE Chi-restraints excluded: chain 2 residue 452 LEU Chi-restraints excluded: chain 2 residue 494 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain c residue 536 THR Chi-restraints excluded: chain c residue 601 LYS Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 260 LEU Chi-restraints excluded: chain d residue 374 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 37 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 chunk 253 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 112 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 1 GLN ** h 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 35 ASN ** 2 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 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 = 0.3403 r_free = 0.3403 target = 0.060350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.043253 restraints weight = 196427.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.044337 restraints weight = 106443.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.044978 restraints weight = 75915.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.045488 restraints weight = 63297.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.045855 restraints weight = 56859.259| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33252 Z= 0.129 Angle : 0.723 15.815 45483 Z= 0.336 Chirality : 0.045 0.249 5442 Planarity : 0.004 0.056 5472 Dihedral : 8.189 76.116 7435 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.01 % Allowed : 13.90 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.31 (0.14), residues: 3777 helix: -0.29 (0.25), residues: 447 sheet: -0.51 (0.14), residues: 1296 loop : -1.21 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 94 TYR 0.015 0.001 TYR A 586 PHE 0.021 0.001 PHE Q 91 TRP 0.034 0.001 TRP d 427 HIS 0.008 0.001 HIS h 35 Details of bonding type rmsd covalent geometry : bond 0.00286 (33045) covalent geometry : angle 0.68607 (44907) SS BOND : bond 0.00225 ( 45) SS BOND : angle 1.59739 ( 90) hydrogen bonds : bond 0.03378 ( 1006) hydrogen bonds : angle 5.52808 ( 2712) link_ALPHA1-2 : bond 0.00308 ( 9) link_ALPHA1-2 : angle 1.81738 ( 27) link_ALPHA1-3 : bond 0.00794 ( 21) link_ALPHA1-3 : angle 1.66398 ( 63) link_ALPHA1-6 : bond 0.00848 ( 12) link_ALPHA1-6 : angle 1.69796 ( 36) link_BETA1-4 : bond 0.00544 ( 69) link_BETA1-4 : angle 2.68594 ( 207) link_NAG-ASN : bond 0.00272 ( 51) link_NAG-ASN : angle 1.93897 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5705.04 seconds wall clock time: 99 minutes 57.28 seconds (5997.28 seconds total)