Starting phenix.real_space_refine on Fri Mar 6 15:43:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ot1_20191/03_2026/6ot1_20191.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ot1_20191/03_2026/6ot1_20191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ot1_20191/03_2026/6ot1_20191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ot1_20191/03_2026/6ot1_20191.map" model { file = "/net/cci-nas-00/data/ceres_data/6ot1_20191/03_2026/6ot1_20191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ot1_20191/03_2026/6ot1_20191.cif" } resolution = 3.5 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= 0.001 sd= 0.106 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 165 5.16 5 C 20226 2.51 5 N 5331 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 162 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32247 Number of models: 1 Model: "" Number of chains: 75 Chain: "B" 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: "G" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "L" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} 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: "O" 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: "E" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "A" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "F" 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: "I" 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: "J" 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: "K" 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: "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: "P" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "M" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 945 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "N" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 855 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "Q" 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: "R" 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: "S" 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: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 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: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" 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: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "v" Number of atoms: 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: 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: "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: 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: "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: "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: 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: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 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: "4" 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: "5" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "6" Number of atoms: 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: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 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: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "AA" Number of atoms: 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: 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: "CA" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "DA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "EA" Number of atoms: 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: "FA" 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: "GA" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.97, per 1000 atoms: 0.25 Number of scatterers: 32247 At special positions: 0 Unit cell: (160.988, 153.475, 155.621, 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 165 16.00 O 6525 8.00 N 5331 7.00 C 20226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.04 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.02 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS q 98 " - pdb=" SG CYS q 100A" distance=2.03 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 87 " distance=2.04 Simple disulfide: pdb=" SG CYS O 598 " - pdb=" SG CYS O 604 " distance=2.02 Simple disulfide: pdb=" SG CYS O 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 98 " - pdb=" SG CYS J 100A" distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS P 501 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 74 " distance=2.04 Simple disulfide: pdb=" SG CYS P 119 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS P 126 " - pdb=" SG CYS P 196 " distance=2.03 Simple disulfide: pdb=" SG CYS P 131 " - pdb=" SG CYS P 157 " distance=2.03 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 433 " distance=2.02 Simple disulfide: pdb=" SG CYS P 218 " - pdb=" SG CYS P 247 " distance=2.03 Simple disulfide: pdb=" SG CYS P 228 " - pdb=" SG CYS P 239 " distance=2.03 Simple disulfide: pdb=" SG CYS P 296 " - pdb=" SG CYS P 331 " distance=2.02 Simple disulfide: pdb=" SG CYS P 378 " - pdb=" SG CYS P 445 " distance=2.03 Simple disulfide: pdb=" SG CYS P 385 " - pdb=" SG CYS P 418 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS S 98 " - pdb=" SG CYS S 100A" distance=2.03 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 87 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN d 4 " - " MAN d 5 " " MAN w 4 " - " MAN w 5 " " MANBA 4 " - " MANBA 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 3 3 " - " MAN 3 4 " " BMA 8 3 " - " MAN 8 4 " " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " BMA i 3 " - " MAN i 4 " " BMA k 3 " - " MAN k 4 " " BMA t 3 " - " MAN t 4 " " BMA w 3 " - " MAN w 4 " " BMA y 3 " - " MAN y 4 " " BMABA 3 " - " MANBA 4 " " BMADA 3 " - " MANDA 4 " " BMAGA 3 " - " MANGA 4 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 3 3 " - " MAN 3 5 " " BMA V 3 " - " MAN V 5 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 5 " " BMA i 3 " - " MAN i 5 " " BMA k 3 " - " MAN k 5 " " BMA w 3 " - " MAN w 6 " " BMA y 3 " - " MAN y 5 " " BMABA 3 " - " MANBA 6 " " BMADA 3 " - " MANDA 5 " " BMAGA 3 " - " MANGA 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 6 1 " - " NAG 6 2 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 8 2 " - " BMA 8 3 " " NAG 9 1 " - " NAG 9 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG 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 " " NAGAA 1 " - " NAGAA 2 " " NAGBA 1 " - " NAGBA 2 " " NAGBA 2 " - " BMABA 3 " " NAGCA 1 " - " NAGCA 2 " " NAGCA 2 " - " BMACA 3 " " NAGDA 1 " - " NAGDA 2 " " NAGDA 2 " - " BMADA 3 " " NAGEA 1 " - " NAGEA 2 " " NAGEA 2 " - " BMAEA 3 " " NAGFA 1 " - " NAGFA 2 " " NAGGA 1 " - " NAGGA 2 " " NAGGA 2 " - " BMAGA 3 " NAG-ASN " NAG 0 1 " - " ASN E 448 " " NAG 1 1 " - " ASN E 276 " " NAG 2 1 " - " ASN P 88 " " NAG 3 1 " - " ASN P 137 " " NAG 4 1 " - " ASN P 156 " " NAG 5 1 " - " ASN P 160 " " NAG 6 1 " - " ASN P 197 " " NAG 7 1 " - " ASN P 234 " " NAG 8 1 " - " ASN P 262 " " NAG 9 1 " - " ASN P 295 " " NAG B 701 " - " ASN B 637 " " NAG D 701 " - " ASN D 637 " " NAG E 625 " - " ASN E 133 " " NAG E 632 " - " ASN E 339 " " NAG E 633 " - " ASN E 355 " " NAG G 625 " - " ASN G 133 " " NAG G 632 " - " ASN G 339 " " NAG G 633 " - " ASN G 355 " " NAG O 701 " - " ASN O 637 " " NAG P 625 " - " ASN P 133 " " NAG P 632 " - " ASN P 339 " " NAG P 633 " - " ASN P 355 " " NAG U 1 " - " ASN G 88 " " NAG V 1 " - " ASN G 137 " " NAG W 1 " - " ASN G 156 " " NAG X 1 " - " ASN G 160 " " NAG Y 1 " - " ASN G 197 " " NAG Z 1 " - " ASN G 234 " " NAG a 1 " - " ASN G 262 " " NAG b 1 " - " ASN G 295 " " NAG c 1 " - " ASN G 301 " " NAG d 1 " - " ASN G 332 " " NAG e 1 " - " ASN G 363 " " NAG f 1 " - " ASN G 386 " " NAG g 1 " - " ASN G 392 " " NAG h 1 " - " ASN G 448 " " NAG i 1 " - " ASN G 276 " " NAG j 1 " - " ASN E 88 " " NAG k 1 " - " ASN E 137 " " NAG l 1 " - " ASN E 156 " " NAG o 1 " - " ASN E 160 " " NAG p 1 " - " ASN E 197 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 262 " " NAG u 1 " - " ASN E 295 " " NAG v 1 " - " ASN E 301 " " NAG w 1 " - " ASN E 332 " " NAG x 1 " - " ASN E 363 " " NAG y 1 " - " ASN E 386 " " NAG z 1 " - " ASN E 392 " " NAGAA 1 " - " ASN P 301 " " NAGBA 1 " - " ASN P 332 " " NAGCA 1 " - " ASN P 363 " " NAGDA 1 " - " ASN P 386 " " NAGEA 1 " - " ASN P 392 " " NAGFA 1 " - " ASN P 448 " " NAGGA 1 " - " ASN P 276 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7086 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 93 sheets defined 11.9% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 removed outlier: 3.894A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.606A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.740A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 removed outlier: 3.826A pdb=" N GLU G 62 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 115 removed outlier: 3.588A pdb=" N HIS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 3.880A pdb=" N LEU G 125 " --> pdb=" O LEU G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 349 removed outlier: 3.691A pdb=" N GLU G 340 " --> pdb=" O ALA G 336 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 354 Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.406A pdb=" N ARG G 429 " --> pdb=" O MET G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 4.089A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.018A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 32 removed outlier: 3.671A pdb=" N ASP m 31 " --> pdb=" O LEU m 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN m 32 " --> pdb=" O VAL m 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 28 through 32' Processing helix chain 'n' and resid 79 through 83 removed outlier: 3.517A pdb=" N GLU n 83 " --> pdb=" O ALA n 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 87 removed outlier: 3.990A pdb=" N THR q 87 " --> pdb=" O PRO q 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 529 through 534 Processing helix chain 'O' and resid 537 through 543 removed outlier: 3.892A pdb=" N ASN O 543 " --> pdb=" O VAL O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA O 578 " --> pdb=" O LYS O 574 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU O 581 " --> pdb=" O GLN O 577 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU O 584 " --> pdb=" O VAL O 580 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP O 589 " --> pdb=" O ARG O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 627 through 636 removed outlier: 3.607A pdb=" N LYS O 633 " --> pdb=" O LEU O 629 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU O 634 " --> pdb=" O GLN O 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER O 636 " --> pdb=" O ASP O 632 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 664 removed outlier: 3.740A pdb=" N GLU O 647 " --> pdb=" O TYR O 643 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU O 648 " --> pdb=" O GLY O 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN O 653 " --> pdb=" O SER O 649 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU O 663 " --> pdb=" O ASP O 659 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP O 664 " --> pdb=" O LEU O 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 removed outlier: 3.827A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 115 removed outlier: 3.587A pdb=" N HIS E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.880A pdb=" N LEU E 125 " --> pdb=" O LEU E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 349 removed outlier: 3.691A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 354 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.408A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 4.088A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR A 87 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 4.018A pdb=" N VAL C 83 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.672A pdb=" N ASP F 31 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN F 32 " --> pdb=" O VAL F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.517A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.990A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.893A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.617A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 584 " --> pdb=" O VAL D 580 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.606A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 636 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 664 removed outlier: 3.741A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 653 " --> pdb=" O SER D 649 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 62 removed outlier: 3.826A pdb=" N GLU P 62 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 115 removed outlier: 3.587A pdb=" N HIS P 105 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE P 109 " --> pdb=" O HIS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 126 removed outlier: 3.881A pdb=" N LEU P 125 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 349 removed outlier: 3.690A pdb=" N GLU P 340 " --> pdb=" O ALA P 336 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS P 347 " --> pdb=" O GLY P 343 " (cutoff:3.500A) Processing helix chain 'P' and resid 349 through 354 Processing helix chain 'P' and resid 425 through 429 removed outlier: 4.407A pdb=" N ARG P 429 " --> pdb=" O MET P 426 " (cutoff:3.500A) Processing helix chain 'P' and resid 475 through 480 removed outlier: 4.088A pdb=" N TRP P 479 " --> pdb=" O MET P 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.593A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.019A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.672A pdb=" N ASP Q 31 " --> pdb=" O LEU Q 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN Q 32 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 28 through 32' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.518A pdb=" N GLU R 83 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 87 removed outlier: 3.991A pdb=" N THR S 87 " --> pdb=" O PRO S 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 7.991A pdb=" N THR B 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL G 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.509A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 92 removed outlier: 3.563A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AA5, first strand: chain 'G' and resid 158 through 162 Processing sheet with id=AA6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 297 through 298 Processing sheet with id=AB1, first strand: chain 'G' and resid 304 through 308 Processing sheet with id=AB2, first strand: chain 'G' and resid 330 through 334 Processing sheet with id=AB3, first strand: chain 'G' and resid 375 through 378 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.561A pdb=" N SER H 70 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.694A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE H 32 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TYR H 52 " --> pdb=" O PHE H 32 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.694A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG H 94 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU L 89 " --> pdb=" O HIS L 34 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR m 33 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR m 105 " --> pdb=" O TYR m 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS m 92 " --> pdb=" O TRP m 101 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP m 101 " --> pdb=" O CYS m 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR m 94 " --> pdb=" O ASP m 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY m 98 " --> pdb=" O TYR m 100M" (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 18 through 22 Processing sheet with id=AC3, first strand: chain 'n' and resid 9 through 13 removed outlier: 3.761A pdb=" N ALA n 84 " --> pdb=" O LEU n 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP n 35 " --> pdb=" O ILE n 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'n' and resid 19 through 20 Processing sheet with id=AC5, first strand: chain 'n' and resid 23 through 26 removed outlier: 3.663A pdb=" N ALA n 71 " --> pdb=" O CYS n 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.365A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N HIS q 35 " --> pdb=" O VAL q 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'q' and resid 10 through 11 removed outlier: 6.365A pdb=" N VAL q 10 " --> pdb=" O VAL q 110 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS q 92 " --> pdb=" O TRP q 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP q 103 " --> pdb=" O CYS q 92 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG q 94 " --> pdb=" O GLN q 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'q' and resid 17 through 19 Processing sheet with id=AD1, first strand: chain 'q' and resid 49 through 52 removed outlier: 3.500A pdb=" N SER q 58 " --> pdb=" O TRP q 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'r' and resid 5 through 6 Processing sheet with id=AD3, first strand: chain 'r' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP r 34 " --> pdb=" O LEU r 46 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR r 48 " --> pdb=" O ARG r 52 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'r' and resid 10 through 13 Processing sheet with id=AD5, first strand: chain 'O' and resid 603 through 609 removed outlier: 7.992A pdb=" N THR O 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL E 38 " --> pdb=" O THR O 606 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL O 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.507A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AD9, first strand: chain 'E' and resid 158 through 162 Processing sheet with id=AE1, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE2, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.790A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.367A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.546A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.790A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AE5, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AE6, first strand: chain 'E' and resid 330 through 334 Processing sheet with id=AE7, first strand: chain 'E' and resid 375 through 378 Processing sheet with id=AE8, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.559A pdb=" N SER A 70 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.692A pdb=" N VAL A 12 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE A 32 " --> pdb=" O TYR A 52 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR A 52 " --> pdb=" O PHE A 32 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.692A pdb=" N VAL A 12 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 94 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AF3, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.584A pdb=" N GLU C 105 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 89 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR F 105 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR F 33 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.503A pdb=" N THR F 105 " --> pdb=" O TYR F 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS F 92 " --> pdb=" O TRP F 101 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TRP F 101 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N THR F 94 " --> pdb=" O ASP F 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY F 98 " --> pdb=" O TYR F 100M" (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 18 through 22 Processing sheet with id=AF7, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.760A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR I 87 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP I 35 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AF9, first strand: chain 'I' and resid 23 through 26 removed outlier: 3.664A pdb=" N ALA I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.364A pdb=" N VAL J 10 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS J 35 " --> pdb=" O VAL J 93 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.364A pdb=" N VAL J 10 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG J 94 " --> pdb=" O GLN J 101 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AG5, first strand: chain 'J' and resid 49 through 52 removed outlier: 3.502A pdb=" N SER J 58 " --> pdb=" O TRP J 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AG7, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP K 34 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR K 48 " --> pdb=" O ARG K 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AG9, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.991A pdb=" N THR D 606 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL P 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 608 " --> pdb=" O VAL P 36 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 45 through 47 removed outlier: 3.510A pdb=" N ILE P 225 " --> pdb=" O VAL P 245 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'P' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU P 91 " --> pdb=" O CYS P 239 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AH4, first strand: chain 'P' and resid 158 through 162 Processing sheet with id=AH5, first strand: chain 'P' and resid 181 through 183 Processing sheet with id=AH6, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY P 451 " --> pdb=" O THR P 290 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N THR P 290 " --> pdb=" O GLY P 451 " (cutoff:3.500A) removed outlier: 11.368A pdb=" N ILE P 453 " --> pdb=" O PHE P 288 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N PHE P 288 " --> pdb=" O ILE P 453 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR P 455 " --> pdb=" O VAL P 286 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N VAL P 286 " --> pdb=" O THR P 455 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'P' and resid 260 through 261 removed outlier: 6.791A pdb=" N LEU P 260 " --> pdb=" O THR P 450 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG P 360 " --> pdb=" O PHE P 468 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 297 through 298 Processing sheet with id=AH9, first strand: chain 'P' and resid 304 through 308 Processing sheet with id=AI1, first strand: chain 'P' and resid 330 through 334 Processing sheet with id=AI2, first strand: chain 'P' and resid 375 through 378 Processing sheet with id=AI3, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.561A pdb=" N SER M 70 " --> pdb=" O ALA M 79 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.691A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE M 32 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR M 52 " --> pdb=" O PHE M 32 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.691A pdb=" N VAL M 12 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG M 94 " --> pdb=" O VAL M 102 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AI7, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.585A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU N 89 " --> pdb=" O HIS N 34 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.502A pdb=" N THR Q 105 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR Q 33 " --> pdb=" O THR Q 95 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP Q 34 " --> pdb=" O TYR Q 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Q' and resid 11 through 12 removed outlier: 3.502A pdb=" N THR Q 105 " --> pdb=" O TYR Q 90 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS Q 92 " --> pdb=" O TRP Q 101 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TRP Q 101 " --> pdb=" O CYS Q 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR Q 94 " --> pdb=" O ASP Q 100Q" (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY Q 98 " --> pdb=" O TYR Q 100M" (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 18 through 22 Processing sheet with id=AJ2, first strand: chain 'R' and resid 9 through 13 removed outlier: 3.760A pdb=" N ALA R 84 " --> pdb=" O LEU R 104 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR R 87 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP R 35 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 19 through 20 Processing sheet with id=AJ4, first strand: chain 'R' and resid 23 through 26 removed outlier: 3.663A pdb=" N ALA R 71 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AJ6, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.362A pdb=" N VAL S 10 " --> pdb=" O VAL S 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS S 35 " --> pdb=" O VAL S 93 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.362A pdb=" N VAL S 10 " --> pdb=" O VAL S 110 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N CYS S 92 " --> pdb=" O TRP S 103 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP S 103 " --> pdb=" O CYS S 92 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG S 94 " --> pdb=" O GLN S 101 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 17 through 19 Processing sheet with id=AJ9, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.500A pdb=" N SER S 58 " --> pdb=" O TRP S 50 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'T' and resid 5 through 6 Processing sheet with id=AK2, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.452A pdb=" N TRP T 34 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR T 48 " --> pdb=" O ARG T 52 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'T' and resid 10 through 13 924 hydrogen bonds defined for protein. 2214 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: 7.49 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9970 1.34 - 1.46: 8484 1.46 - 1.58: 14276 1.58 - 1.70: 0 1.70 - 1.82: 216 Bond restraints: 32946 Sorted by residual: bond pdb=" C THR G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 1.334 1.379 -0.045 8.40e-03 1.42e+04 2.89e+01 bond pdb=" C THR P 123 " pdb=" N PRO P 124 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.73e+01 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.334 1.377 -0.043 8.40e-03 1.42e+04 2.63e+01 bond pdb=" C1 NAG 2 1 " pdb=" O5 NAG 2 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.15e+00 bond pdb=" C1 BMA z 3 " pdb=" C2 BMA z 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 6.12e+00 ... (remaining 32941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 42345 1.96 - 3.92: 1975 3.92 - 5.88: 310 5.88 - 7.84: 116 7.84 - 9.80: 44 Bond angle restraints: 44790 Sorted by residual: angle pdb=" C GLY L 68 " pdb=" N THR L 69 " pdb=" CA THR L 69 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C GLY C 68 " pdb=" N THR C 69 " pdb=" CA THR C 69 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C GLY N 68 " pdb=" N THR N 69 " pdb=" CA THR N 69 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C CYS J 98 " pdb=" N ASP J 99 " pdb=" CA ASP J 99 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C CYS q 98 " pdb=" N ASP q 99 " pdb=" CA ASP q 99 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 ... (remaining 44785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 19477 21.69 - 43.39: 1540 43.39 - 65.08: 238 65.08 - 86.78: 177 86.78 - 108.47: 99 Dihedral angle restraints: 21531 sinusoidal: 10467 harmonic: 11064 Sorted by residual: dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.91 65.91 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.90 65.90 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CB CYS P 119 " pdb=" SG CYS P 119 " pdb=" SG CYS P 205 " pdb=" CB CYS P 205 " ideal model delta sinusoidal sigma weight residual -86.00 -151.87 65.87 1 1.00e+01 1.00e-02 5.68e+01 ... (remaining 21528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4669 0.087 - 0.175: 688 0.175 - 0.262: 52 0.262 - 0.350: 30 0.350 - 0.437: 6 Chirality restraints: 5445 Sorted by residual: chirality pdb=" C2 NAG V 1 " pdb=" C1 NAG V 1 " pdb=" C3 NAG V 1 " pdb=" N2 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.05 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" C2 NAG 3 1 " pdb=" C1 NAG 3 1 " pdb=" C3 NAG 3 1 " pdb=" N2 NAG 3 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C2 NAG k 1 " pdb=" C1 NAG k 1 " pdb=" C3 NAG k 1 " pdb=" N2 NAG k 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.06 -0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 5442 not shown) Planarity restraints: 5547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 275 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C GLU G 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU G 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN G 276 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 275 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLU P 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU P 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN P 276 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 275 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C GLU E 275 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU E 275 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN E 276 " -0.016 2.00e-02 2.50e+03 ... (remaining 5544 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 393 2.59 - 3.17: 25306 3.17 - 3.75: 47473 3.75 - 4.32: 64453 4.32 - 4.90: 107153 Nonbonded interactions: 244778 Sorted by model distance: nonbonded pdb=" OE1 GLU O 647 " pdb=" NH2 ARG D 542 " model vdw 2.015 3.120 nonbonded pdb=" NH2 ARG B 542 " pdb=" OE1 GLU D 647 " model vdw 2.021 3.120 nonbonded pdb=" CB ASP q 76B" pdb=" OH TYR E 318 " model vdw 2.032 3.440 nonbonded pdb=" OH TYR G 318 " pdb=" CB ASP S 76B" model vdw 2.048 3.440 nonbonded pdb=" OE1 GLU B 647 " pdb=" NH2 ARG O 542 " model vdw 2.048 3.120 ... (remaining 244773 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: 0.07 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '9' selection = chain 'AA' selection = chain 'FA' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'h' selection = chain 'j' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 'u' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'DA' selection = chain 'GA' selection = chain 'V' selection = chain 'f' selection = chain 'i' selection = chain 'k' selection = chain 'y' } ncs_group { reference = chain '4' selection = chain 'CA' selection = chain 'EA' selection = chain 'W' selection = chain 'e' selection = chain 'g' selection = chain 'l' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain '8' selection = chain 'a' selection = chain 't' } ncs_group { reference = chain 'A' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'BA' selection = chain 'd' selection = chain 'w' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'Q' selection = chain 'm' } ncs_group { reference = chain 'I' selection = chain 'R' selection = chain 'n' } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'q' } ncs_group { reference = chain 'K' selection = chain 'T' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.080 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.030 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.180 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 33159 Z= 0.353 Angle : 1.066 16.616 45372 Z= 0.525 Chirality : 0.063 0.437 5445 Planarity : 0.007 0.064 5490 Dihedral : 18.251 108.471 14274 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.72 % Allowed : 9.69 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -4.15 (0.11), residues: 3801 helix: -4.64 (0.10), residues: 387 sheet: -2.13 (0.14), residues: 1230 loop : -2.84 (0.10), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 327 TYR 0.013 0.002 TYR Q 100M PHE 0.031 0.002 PHE S 100D TRP 0.019 0.002 TRP E 112 HIS 0.006 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00749 (32946) covalent geometry : angle 1.01029 (44790) SS BOND : bond 0.00548 ( 57) SS BOND : angle 2.22938 ( 114) hydrogen bonds : bond 0.26641 ( 870) hydrogen bonds : angle 9.84750 ( 2214) link_ALPHA1-2 : bond 0.00041 ( 3) link_ALPHA1-2 : angle 1.75686 ( 9) link_ALPHA1-3 : bond 0.00521 ( 15) link_ALPHA1-3 : angle 2.52274 ( 45) link_ALPHA1-6 : bond 0.00393 ( 12) link_ALPHA1-6 : angle 1.60195 ( 36) link_BETA1-4 : bond 0.01035 ( 69) link_BETA1-4 : angle 2.68981 ( 207) link_NAG-ASN : bond 0.00966 ( 57) link_NAG-ASN : angle 4.46696 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 434 time to evaluate : 1.293 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: B 519 PHE cc_start: 0.8400 (m-80) cc_final: 0.8016 (m-10) REVERT: B 654 GLU cc_start: 0.8443 (tp30) cc_final: 0.8176 (tp30) REVERT: B 657 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8302 (tm-30) REVERT: G 272 ILE cc_start: 0.8932 (pt) cc_final: 0.8458 (mt) REVERT: G 426 MET cc_start: 0.7357 (mmm) cc_final: 0.7137 (mmt) REVERT: H 36 TRP cc_start: 0.2994 (m100) cc_final: 0.2702 (m100) REVERT: L 50 GLU cc_start: 0.4860 (mt-10) cc_final: 0.4481 (mm-30) REVERT: m 103 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8096 (mppt) REVERT: r 17 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 32 PHE cc_start: 0.7258 (m-80) cc_final: 0.6722 (m-10) REVERT: C 50 GLU cc_start: 0.5097 (mt-10) cc_final: 0.4727 (mm-30) REVERT: F 13 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7757 (mmmt) REVERT: F 103 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8165 (mppt) REVERT: I 49 TYR cc_start: 0.8377 (p90) cc_final: 0.8108 (p90) REVERT: D 519 PHE cc_start: 0.8575 (m-80) cc_final: 0.8237 (m-10) REVERT: P 439 ILE cc_start: 0.8856 (pt) cc_final: 0.8563 (pt) REVERT: N 50 GLU cc_start: 0.4691 (mt-10) cc_final: 0.4323 (mm-30) REVERT: Q 103 LYS cc_start: 0.8159 (mmmm) cc_final: 0.7945 (mppt) REVERT: T 11 LEU cc_start: 0.9046 (tp) cc_final: 0.8792 (tt) REVERT: T 78 ASP cc_start: 0.8748 (t70) cc_final: 0.8489 (t70) outliers start: 24 outliers final: 8 residues processed: 458 average time/residue: 0.2185 time to fit residues: 154.8670 Evaluate side-chains 303 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 295 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 575 GLN G 67 ASN G 103 GLN G 183 GLN G 203 GLN H 77 GLN L 93 GLN ** m 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 GLN n 38 GLN O 575 GLN E 67 ASN E 103 GLN E 183 GLN E 203 GLN A 77 GLN C 93 GLN ** F 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN I 38 GLN D 575 GLN P 67 ASN P 103 GLN P 183 GLN P 203 GLN M 3 GLN M 77 GLN N 93 GLN ** Q 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN R 38 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.107089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.066345 restraints weight = 80454.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068429 restraints weight = 44993.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069793 restraints weight = 32585.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070595 restraints weight = 27150.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.070979 restraints weight = 24563.596| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33159 Z= 0.148 Angle : 0.754 12.185 45372 Z= 0.364 Chirality : 0.047 0.276 5445 Planarity : 0.005 0.057 5490 Dihedral : 14.220 82.106 7343 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.00 % Allowed : 14.47 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -3.44 (0.12), residues: 3801 helix: -3.40 (0.17), residues: 414 sheet: -1.71 (0.14), residues: 1209 loop : -2.43 (0.11), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 38 TYR 0.018 0.001 TYR E 318 PHE 0.019 0.002 PHE S 100D TRP 0.014 0.001 TRP D 571 HIS 0.003 0.001 HIS H 31B Details of bonding type rmsd covalent geometry : bond 0.00321 (32946) covalent geometry : angle 0.70920 (44790) SS BOND : bond 0.00336 ( 57) SS BOND : angle 1.85132 ( 114) hydrogen bonds : bond 0.04647 ( 870) hydrogen bonds : angle 6.66106 ( 2214) link_ALPHA1-2 : bond 0.00804 ( 3) link_ALPHA1-2 : angle 1.74912 ( 9) link_ALPHA1-3 : bond 0.01024 ( 15) link_ALPHA1-3 : angle 2.40729 ( 45) link_ALPHA1-6 : bond 0.00564 ( 12) link_ALPHA1-6 : angle 1.80454 ( 36) link_BETA1-4 : bond 0.00543 ( 69) link_BETA1-4 : angle 2.02818 ( 207) link_NAG-ASN : bond 0.00368 ( 57) link_NAG-ASN : angle 3.09936 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 341 time to evaluate : 1.042 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: B 519 PHE cc_start: 0.8155 (m-80) cc_final: 0.7933 (m-10) REVERT: G 125 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8439 (tt) REVERT: G 203 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: G 272 ILE cc_start: 0.8886 (pt) cc_final: 0.8512 (mt) REVERT: L 50 GLU cc_start: 0.4719 (mt-10) cc_final: 0.4498 (mm-30) REVERT: m 32 ASN cc_start: 0.8610 (m-40) cc_final: 0.8336 (m110) REVERT: m 43 LYS cc_start: 0.9369 (mmmm) cc_final: 0.9105 (mtmt) REVERT: m 103 LYS cc_start: 0.8452 (mmmm) cc_final: 0.8182 (mppt) REVERT: n 49 TYR cc_start: 0.8383 (p90) cc_final: 0.8118 (p90) REVERT: n 87 TYR cc_start: 0.8337 (m-80) cc_final: 0.7815 (m-80) REVERT: q 76 ASP cc_start: 0.8038 (t0) cc_final: 0.7824 (t0) REVERT: q 100 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7680 (t80) REVERT: E 33 ASN cc_start: 0.7998 (p0) cc_final: 0.7541 (p0) REVERT: C 50 GLU cc_start: 0.5032 (mt-10) cc_final: 0.4810 (mm-30) REVERT: F 43 LYS cc_start: 0.9363 (mmmm) cc_final: 0.9129 (mttt) REVERT: F 103 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8211 (mppt) REVERT: J 99 ASP cc_start: 0.8913 (p0) cc_final: 0.8713 (p0) REVERT: K 1 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: K 98 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7491 (tm-30) REVERT: P 33 ASN cc_start: 0.8076 (p0) cc_final: 0.7855 (p0) REVERT: P 255 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8767 (m) REVERT: N 50 GLU cc_start: 0.4960 (mt-10) cc_final: 0.4643 (mm-30) REVERT: Q 32 ASN cc_start: 0.8473 (m-40) cc_final: 0.8222 (m-40) REVERT: Q 103 LYS cc_start: 0.8302 (mmmm) cc_final: 0.8085 (mppt) REVERT: S 100 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7637 (t80) outliers start: 67 outliers final: 26 residues processed: 394 average time/residue: 0.2290 time to fit residues: 141.4504 Evaluate side-chains 326 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 294 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 42 VAL Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 20 optimal weight: 2.9990 chunk 315 optimal weight: 30.0000 chunk 174 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 347 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 363 optimal weight: 0.9980 chunk 336 optimal weight: 10.0000 chunk 328 optimal weight: 30.0000 chunk 163 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 93 GLN D 543 ASN M 5 GLN N 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.106438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.065346 restraints weight = 82313.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067438 restraints weight = 46486.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068736 restraints weight = 33840.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.069570 restraints weight = 28572.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069967 restraints weight = 25812.380| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 33159 Z= 0.168 Angle : 0.730 11.205 45372 Z= 0.349 Chirality : 0.047 0.284 5445 Planarity : 0.004 0.058 5490 Dihedral : 12.591 80.996 7342 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.69 % Allowed : 15.87 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.99 (0.12), residues: 3801 helix: -2.60 (0.21), residues: 396 sheet: -1.50 (0.14), residues: 1248 loop : -2.19 (0.12), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 30 TYR 0.015 0.001 TYR G 318 PHE 0.041 0.002 PHE L 98 TRP 0.012 0.001 TRP P 96 HIS 0.005 0.001 HIS m 3 Details of bonding type rmsd covalent geometry : bond 0.00377 (32946) covalent geometry : angle 0.69233 (44790) SS BOND : bond 0.00639 ( 57) SS BOND : angle 1.44119 ( 114) hydrogen bonds : bond 0.03961 ( 870) hydrogen bonds : angle 6.02244 ( 2214) link_ALPHA1-2 : bond 0.00518 ( 3) link_ALPHA1-2 : angle 1.78993 ( 9) link_ALPHA1-3 : bond 0.01071 ( 15) link_ALPHA1-3 : angle 1.88235 ( 45) link_ALPHA1-6 : bond 0.00534 ( 12) link_ALPHA1-6 : angle 1.74820 ( 36) link_BETA1-4 : bond 0.00531 ( 69) link_BETA1-4 : angle 1.94524 ( 207) link_NAG-ASN : bond 0.00433 ( 57) link_NAG-ASN : angle 2.86554 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 315 time to evaluate : 1.246 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: B 519 PHE cc_start: 0.8198 (m-80) cc_final: 0.7961 (m-10) REVERT: B 530 MET cc_start: 0.8260 (mtt) cc_final: 0.7953 (mtt) REVERT: G 161 MET cc_start: 0.7634 (tpp) cc_final: 0.7402 (ttm) REVERT: G 272 ILE cc_start: 0.8888 (pt) cc_final: 0.8541 (mt) REVERT: L 50 GLU cc_start: 0.5081 (mt-10) cc_final: 0.4834 (mm-30) REVERT: m 32 ASN cc_start: 0.8427 (m-40) cc_final: 0.8203 (m110) REVERT: m 103 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8183 (mppt) REVERT: n 87 TYR cc_start: 0.8328 (m-80) cc_final: 0.7725 (m-80) REVERT: q 76 ASP cc_start: 0.8023 (t0) cc_final: 0.7632 (t0) REVERT: q 100 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7712 (t80) REVERT: O 663 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8706 (pp) REVERT: E 33 ASN cc_start: 0.8039 (p0) cc_final: 0.7614 (p0) REVERT: C 4 MET cc_start: 0.0042 (mmm) cc_final: -0.0237 (mmm) REVERT: C 50 GLU cc_start: 0.5097 (mt-10) cc_final: 0.4857 (mm-30) REVERT: F 103 LYS cc_start: 0.8444 (mmmm) cc_final: 0.8187 (mppt) REVERT: I 54 ARG cc_start: 0.8598 (ptt-90) cc_final: 0.8220 (ptt180) REVERT: K 1 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: D 519 PHE cc_start: 0.8336 (m-10) cc_final: 0.8121 (m-10) REVERT: P 33 ASN cc_start: 0.8047 (p0) cc_final: 0.7820 (p0) REVERT: P 255 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8808 (m) REVERT: N 50 GLU cc_start: 0.4836 (mt-10) cc_final: 0.4553 (mm-30) REVERT: Q 30 ARG cc_start: 0.8860 (ttp-110) cc_final: 0.8524 (tpp80) REVERT: Q 32 ASN cc_start: 0.8283 (m-40) cc_final: 0.7918 (m-40) REVERT: Q 103 LYS cc_start: 0.8343 (mmmm) cc_final: 0.8126 (mppt) REVERT: S 100 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7644 (t80) outliers start: 90 outliers final: 48 residues processed: 387 average time/residue: 0.2050 time to fit residues: 126.3797 Evaluate side-chains 342 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 46 GLU Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 100 TYR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 570 VAL Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain O residue 663 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 255 VAL Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 98 CYS Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 357 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 335 optimal weight: 0.0670 chunk 71 optimal weight: 0.1980 chunk 317 optimal weight: 50.0000 chunk 50 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 181 optimal weight: 0.9990 chunk 74 optimal weight: 40.0000 chunk 314 optimal weight: 0.0770 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN E 203 GLN P 203 GLN M 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.107442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.071925 restraints weight = 80219.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.070908 restraints weight = 57043.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071531 restraints weight = 48675.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.071596 restraints weight = 41794.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.071805 restraints weight = 35644.759| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33159 Z= 0.132 Angle : 0.702 10.910 45372 Z= 0.335 Chirality : 0.046 0.277 5445 Planarity : 0.004 0.057 5490 Dihedral : 11.093 78.005 7340 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.93 % Allowed : 17.16 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.74 (0.13), residues: 3801 helix: -2.16 (0.23), residues: 396 sheet: -1.36 (0.14), residues: 1236 loop : -2.05 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 38 TYR 0.016 0.001 TYR A 59 PHE 0.041 0.002 PHE L 98 TRP 0.019 0.001 TRP H 36 HIS 0.006 0.001 HIS m 3 Details of bonding type rmsd covalent geometry : bond 0.00292 (32946) covalent geometry : angle 0.66778 (44790) SS BOND : bond 0.00422 ( 57) SS BOND : angle 1.43625 ( 114) hydrogen bonds : bond 0.03399 ( 870) hydrogen bonds : angle 5.57653 ( 2214) link_ALPHA1-2 : bond 0.00539 ( 3) link_ALPHA1-2 : angle 1.55899 ( 9) link_ALPHA1-3 : bond 0.01065 ( 15) link_ALPHA1-3 : angle 1.88769 ( 45) link_ALPHA1-6 : bond 0.00533 ( 12) link_ALPHA1-6 : angle 1.72735 ( 36) link_BETA1-4 : bond 0.00492 ( 69) link_BETA1-4 : angle 1.79487 ( 207) link_NAG-ASN : bond 0.00348 ( 57) link_NAG-ASN : angle 2.63094 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 323 time to evaluate : 1.203 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: B 657 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8237 (tm-30) REVERT: G 161 MET cc_start: 0.7608 (tpp) cc_final: 0.7348 (ttm) REVERT: G 272 ILE cc_start: 0.8887 (pt) cc_final: 0.8593 (mt) REVERT: m 103 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8188 (mppt) REVERT: n 87 TYR cc_start: 0.8300 (m-80) cc_final: 0.7746 (m-10) REVERT: E 33 ASN cc_start: 0.8118 (p0) cc_final: 0.7868 (p0) REVERT: F 43 LYS cc_start: 0.9379 (mmmm) cc_final: 0.9074 (mtmt) REVERT: F 103 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8258 (mppt) REVERT: I 54 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.8263 (ptt90) REVERT: J 100 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8164 (t80) REVERT: K 1 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: K 32 MET cc_start: 0.8463 (tpt) cc_final: 0.7332 (tpp) REVERT: K 78 ASP cc_start: 0.8502 (t70) cc_final: 0.8169 (t70) REVERT: K 98 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7489 (tm-30) REVERT: Q 32 ASN cc_start: 0.8328 (m-40) cc_final: 0.8027 (m-40) REVERT: Q 103 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8168 (mppt) REVERT: S 100 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.7797 (t80) outliers start: 98 outliers final: 50 residues processed: 406 average time/residue: 0.2077 time to fit residues: 134.8705 Evaluate side-chains 337 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 284 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 280 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 345 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 chunk 374 optimal weight: 6.9990 chunk 365 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 32 ASN E 203 GLN A 3 GLN A 5 GLN C 90 GLN P 33 ASN S 101 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.108087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.067258 restraints weight = 80608.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.069412 restraints weight = 45182.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070789 restraints weight = 32661.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.071564 restraints weight = 27158.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071926 restraints weight = 24690.534| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33159 Z= 0.121 Angle : 0.679 10.602 45372 Z= 0.324 Chirality : 0.046 0.276 5445 Planarity : 0.004 0.058 5490 Dihedral : 9.946 75.985 7339 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.84 % Allowed : 17.64 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.13), residues: 3801 helix: -1.74 (0.25), residues: 396 sheet: -1.22 (0.14), residues: 1254 loop : -1.95 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.017 0.001 TYR A 59 PHE 0.037 0.001 PHE C 98 TRP 0.018 0.001 TRP H 36 HIS 0.006 0.001 HIS m 3 Details of bonding type rmsd covalent geometry : bond 0.00269 (32946) covalent geometry : angle 0.64739 (44790) SS BOND : bond 0.00312 ( 57) SS BOND : angle 1.40230 ( 114) hydrogen bonds : bond 0.03137 ( 870) hydrogen bonds : angle 5.20035 ( 2214) link_ALPHA1-2 : bond 0.00481 ( 3) link_ALPHA1-2 : angle 1.52981 ( 9) link_ALPHA1-3 : bond 0.01106 ( 15) link_ALPHA1-3 : angle 1.76530 ( 45) link_ALPHA1-6 : bond 0.00548 ( 12) link_ALPHA1-6 : angle 1.90101 ( 36) link_BETA1-4 : bond 0.00496 ( 69) link_BETA1-4 : angle 1.70913 ( 207) link_NAG-ASN : bond 0.00318 ( 57) link_NAG-ASN : angle 2.47845 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 314 time to evaluate : 1.226 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: G 161 MET cc_start: 0.7735 (tpp) cc_final: 0.7445 (ttm) REVERT: G 272 ILE cc_start: 0.8914 (pt) cc_final: 0.8628 (mt) REVERT: m 43 LYS cc_start: 0.9210 (mmmm) cc_final: 0.8969 (mtpt) REVERT: O 519 PHE cc_start: 0.7987 (m-10) cc_final: 0.7776 (m-10) REVERT: O 626 MET cc_start: 0.8056 (mtp) cc_final: 0.7855 (mtp) REVERT: E 33 ASN cc_start: 0.7949 (p0) cc_final: 0.7661 (p0) REVERT: C 90 GLN cc_start: 0.4600 (OUTLIER) cc_final: 0.3885 (pm20) REVERT: F 30 ARG cc_start: 0.8715 (ttp-110) cc_final: 0.8331 (tpp80) REVERT: F 103 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8217 (mppt) REVERT: I 49 TYR cc_start: 0.8398 (p90) cc_final: 0.8116 (p90) REVERT: I 54 ARG cc_start: 0.8562 (ptt-90) cc_final: 0.8276 (ptt180) REVERT: J 100 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7512 (t80) REVERT: K 1 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7533 (pt0) REVERT: K 98 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 657 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8276 (pp20) REVERT: P 302 ASN cc_start: 0.8715 (t0) cc_final: 0.8418 (t0) REVERT: Q 13 LYS cc_start: 0.8289 (mmmt) cc_final: 0.8037 (mmmt) REVERT: Q 32 ASN cc_start: 0.8157 (m-40) cc_final: 0.7880 (m-40) REVERT: Q 43 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8919 (mtpt) REVERT: Q 103 LYS cc_start: 0.8330 (mmmm) cc_final: 0.8121 (mppt) REVERT: S 100 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7747 (t80) outliers start: 95 outliers final: 57 residues processed: 392 average time/residue: 0.2083 time to fit residues: 131.3831 Evaluate side-chains 341 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 280 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 213 ILE Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 191 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 0.6980 chunk 304 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 chunk 335 optimal weight: 20.0000 chunk 310 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30EHIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.106644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.065487 restraints weight = 80515.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067548 restraints weight = 45451.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.068865 restraints weight = 33285.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.069690 restraints weight = 28002.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070085 restraints weight = 25403.908| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33159 Z= 0.185 Angle : 0.711 10.417 45372 Z= 0.338 Chirality : 0.046 0.286 5445 Planarity : 0.004 0.056 5490 Dihedral : 9.775 77.078 7339 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.23 % Allowed : 18.89 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.13), residues: 3801 helix: -1.63 (0.25), residues: 402 sheet: -1.13 (0.15), residues: 1254 loop : -1.89 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.017 0.001 TYR A 59 PHE 0.030 0.002 PHE C 98 TRP 0.017 0.001 TRP H 36 HIS 0.005 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00422 (32946) covalent geometry : angle 0.67907 (44790) SS BOND : bond 0.00364 ( 57) SS BOND : angle 1.36476 ( 114) hydrogen bonds : bond 0.03205 ( 870) hydrogen bonds : angle 5.13819 ( 2214) link_ALPHA1-2 : bond 0.00337 ( 3) link_ALPHA1-2 : angle 1.74767 ( 9) link_ALPHA1-3 : bond 0.01083 ( 15) link_ALPHA1-3 : angle 1.84815 ( 45) link_ALPHA1-6 : bond 0.00520 ( 12) link_ALPHA1-6 : angle 1.83682 ( 36) link_BETA1-4 : bond 0.00486 ( 69) link_BETA1-4 : angle 1.72369 ( 207) link_NAG-ASN : bond 0.00447 ( 57) link_NAG-ASN : angle 2.58984 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 287 time to evaluate : 1.305 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: G 161 MET cc_start: 0.7803 (tpp) cc_final: 0.7488 (ttm) REVERT: G 272 ILE cc_start: 0.8956 (pt) cc_final: 0.8645 (mt) REVERT: H 32 PHE cc_start: 0.6891 (m-80) cc_final: 0.6344 (m-10) REVERT: m 30 ARG cc_start: 0.8794 (mtp-110) cc_final: 0.8461 (mmm-85) REVERT: m 53 ASP cc_start: 0.8406 (p0) cc_final: 0.8113 (p0) REVERT: E 33 ASN cc_start: 0.7969 (p0) cc_final: 0.7685 (p0) REVERT: E 95 MET cc_start: 0.8309 (ptm) cc_final: 0.7597 (ttp) REVERT: C 6 GLN cc_start: 0.4464 (OUTLIER) cc_final: 0.3344 (mm-40) REVERT: F 103 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8215 (mppt) REVERT: I 49 TYR cc_start: 0.8495 (p90) cc_final: 0.8241 (p90) REVERT: I 54 ARG cc_start: 0.8609 (ptt-90) cc_final: 0.8311 (ptt90) REVERT: J 100 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7655 (t80) REVERT: K 1 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: K 78 ASP cc_start: 0.8366 (t70) cc_final: 0.7882 (t0) REVERT: K 98 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7643 (tm-30) REVERT: Q 32 ASN cc_start: 0.8189 (m-40) cc_final: 0.7761 (m-40) REVERT: Q 100 MET cc_start: 0.8846 (mpp) cc_final: 0.8602 (mpp) REVERT: Q 103 LYS cc_start: 0.8339 (mmmm) cc_final: 0.8129 (mppt) REVERT: S 100 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7850 (t80) outliers start: 108 outliers final: 73 residues processed: 376 average time/residue: 0.2135 time to fit residues: 127.9952 Evaluate side-chains 353 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 276 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 98 CYS Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 140 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 243 optimal weight: 0.0170 chunk 261 optimal weight: 3.9990 chunk 199 optimal weight: 40.0000 chunk 49 optimal weight: 4.9990 chunk 353 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN m 97 HIS ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 HIS P 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.107071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.066012 restraints weight = 80945.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.068054 restraints weight = 45753.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.069371 restraints weight = 33387.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070059 restraints weight = 27964.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070641 restraints weight = 25450.288| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33159 Z= 0.151 Angle : 0.689 10.362 45372 Z= 0.328 Chirality : 0.046 0.284 5445 Planarity : 0.004 0.057 5490 Dihedral : 9.510 75.658 7339 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.99 % Allowed : 20.00 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.13), residues: 3801 helix: -1.49 (0.25), residues: 402 sheet: -0.92 (0.15), residues: 1194 loop : -1.87 (0.12), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 38 TYR 0.018 0.001 TYR A 59 PHE 0.019 0.001 PHE q 91 TRP 0.029 0.001 TRP H 34 HIS 0.005 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00342 (32946) covalent geometry : angle 0.65860 (44790) SS BOND : bond 0.00336 ( 57) SS BOND : angle 1.35125 ( 114) hydrogen bonds : bond 0.03090 ( 870) hydrogen bonds : angle 4.94833 ( 2214) link_ALPHA1-2 : bond 0.00442 ( 3) link_ALPHA1-2 : angle 1.59353 ( 9) link_ALPHA1-3 : bond 0.01067 ( 15) link_ALPHA1-3 : angle 1.70498 ( 45) link_ALPHA1-6 : bond 0.00564 ( 12) link_ALPHA1-6 : angle 1.79148 ( 36) link_BETA1-4 : bond 0.00467 ( 69) link_BETA1-4 : angle 1.63486 ( 207) link_NAG-ASN : bond 0.00383 ( 57) link_NAG-ASN : angle 2.48250 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 293 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: G 161 MET cc_start: 0.7738 (tpp) cc_final: 0.7386 (ttm) REVERT: G 272 ILE cc_start: 0.8924 (pt) cc_final: 0.8635 (mt) REVERT: H 4 LEU cc_start: 0.6298 (mp) cc_final: 0.6055 (tp) REVERT: H 32 PHE cc_start: 0.6895 (m-80) cc_final: 0.6525 (m-10) REVERT: L 6 GLN cc_start: 0.3920 (OUTLIER) cc_final: 0.2557 (mm-40) REVERT: m 30 ARG cc_start: 0.8807 (mtp-110) cc_final: 0.8477 (mmm-85) REVERT: m 43 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8909 (mtpt) REVERT: m 53 ASP cc_start: 0.8382 (p0) cc_final: 0.8108 (p0) REVERT: E 33 ASN cc_start: 0.7956 (p0) cc_final: 0.7678 (p0) REVERT: E 95 MET cc_start: 0.8406 (ptm) cc_final: 0.7905 (ttp) REVERT: C 36 TYR cc_start: 0.5140 (m-10) cc_final: 0.4835 (m-10) REVERT: F 16 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6913 (tm-30) REVERT: F 30 ARG cc_start: 0.8764 (ttp-110) cc_final: 0.8209 (tpp80) REVERT: F 103 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8226 (mppt) REVERT: I 49 TYR cc_start: 0.8471 (p90) cc_final: 0.8255 (p90) REVERT: I 54 ARG cc_start: 0.8624 (ptt-90) cc_final: 0.8355 (ptt90) REVERT: I 79 GLU cc_start: 0.8516 (pm20) cc_final: 0.8307 (pm20) REVERT: J 100 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7670 (t80) REVERT: K 1 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: K 98 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7613 (tm-30) REVERT: P 95 MET cc_start: 0.8330 (ptm) cc_final: 0.7827 (ttm) REVERT: N 6 GLN cc_start: 0.3991 (OUTLIER) cc_final: 0.3051 (mm-40) REVERT: Q 32 ASN cc_start: 0.8178 (m-40) cc_final: 0.7757 (m-40) REVERT: Q 43 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8909 (mtpt) REVERT: Q 103 LYS cc_start: 0.8330 (mmmm) cc_final: 0.8124 (mppt) REVERT: S 100 TYR cc_start: 0.8380 (OUTLIER) cc_final: 0.7889 (t80) outliers start: 100 outliers final: 76 residues processed: 372 average time/residue: 0.2178 time to fit residues: 129.8124 Evaluate side-chains 359 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 278 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 467 THR Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 80 MET Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 222 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 262 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 232 optimal weight: 6.9990 chunk 301 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 27 GLN C 90 GLN F 1 GLN F 97 HIS K 27 GLN P 33 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS Q 97 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.105524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.064152 restraints weight = 81120.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.066196 restraints weight = 46182.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.067502 restraints weight = 33840.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.068265 restraints weight = 28498.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.068643 restraints weight = 25949.528| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 33159 Z= 0.222 Angle : 0.740 10.493 45372 Z= 0.352 Chirality : 0.047 0.292 5445 Planarity : 0.004 0.056 5490 Dihedral : 9.546 77.384 7339 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.20 % Allowed : 20.57 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.13), residues: 3801 helix: -1.39 (0.25), residues: 384 sheet: -1.08 (0.15), residues: 1269 loop : -1.79 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.018 0.001 TYR A 59 PHE 0.025 0.002 PHE q 91 TRP 0.038 0.001 TRP M 36 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00508 (32946) covalent geometry : angle 0.70825 (44790) SS BOND : bond 0.00345 ( 57) SS BOND : angle 1.48392 ( 114) hydrogen bonds : bond 0.03325 ( 870) hydrogen bonds : angle 5.06400 ( 2214) link_ALPHA1-2 : bond 0.00291 ( 3) link_ALPHA1-2 : angle 1.87686 ( 9) link_ALPHA1-3 : bond 0.01017 ( 15) link_ALPHA1-3 : angle 1.78933 ( 45) link_ALPHA1-6 : bond 0.00546 ( 12) link_ALPHA1-6 : angle 1.80749 ( 36) link_BETA1-4 : bond 0.00490 ( 69) link_BETA1-4 : angle 1.73561 ( 207) link_NAG-ASN : bond 0.00561 ( 57) link_NAG-ASN : angle 2.66251 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 284 time to evaluate : 1.288 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: G 161 MET cc_start: 0.7892 (tpp) cc_final: 0.7533 (ttm) REVERT: G 272 ILE cc_start: 0.8961 (pt) cc_final: 0.8630 (mt) REVERT: H 32 PHE cc_start: 0.6953 (m-80) cc_final: 0.6571 (m-10) REVERT: L 6 GLN cc_start: 0.4264 (OUTLIER) cc_final: 0.2843 (mm110) REVERT: m 30 ARG cc_start: 0.8810 (mtp-110) cc_final: 0.8471 (mmm-85) REVERT: m 53 ASP cc_start: 0.8421 (p0) cc_final: 0.8173 (p0) REVERT: E 33 ASN cc_start: 0.7965 (p0) cc_final: 0.7694 (p0) REVERT: E 95 MET cc_start: 0.8440 (ptm) cc_final: 0.7942 (ttp) REVERT: C 6 GLN cc_start: 0.4678 (OUTLIER) cc_final: 0.3552 (mm-40) REVERT: F 16 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6988 (tm-30) REVERT: F 30 ARG cc_start: 0.8784 (ttp-110) cc_final: 0.8206 (tpp80) REVERT: F 103 LYS cc_start: 0.8466 (mmmm) cc_final: 0.8199 (mppt) REVERT: J 100 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7714 (t80) REVERT: K 1 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7462 (pt0) REVERT: K 98 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7626 (tm-30) REVERT: P 95 MET cc_start: 0.8420 (ptm) cc_final: 0.8127 (ttp) REVERT: N 6 GLN cc_start: 0.4287 (OUTLIER) cc_final: 0.3446 (mm-40) REVERT: Q 32 ASN cc_start: 0.8198 (m-40) cc_final: 0.7701 (m-40) REVERT: Q 43 LYS cc_start: 0.9225 (mmmm) cc_final: 0.8893 (mtpt) REVERT: Q 96 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8724 (mmmt) REVERT: S 100 TYR cc_start: 0.8336 (OUTLIER) cc_final: 0.7925 (t80) REVERT: T 32 MET cc_start: 0.8267 (tpt) cc_final: 0.7193 (tpp) outliers start: 107 outliers final: 81 residues processed: 369 average time/residue: 0.2122 time to fit residues: 125.6961 Evaluate side-chains 353 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 266 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 9.9990 chunk 349 optimal weight: 0.6980 chunk 377 optimal weight: 3.9990 chunk 330 optimal weight: 40.0000 chunk 253 optimal weight: 5.9990 chunk 351 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 198 optimal weight: 7.9990 chunk 293 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.106149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071711 restraints weight = 80476.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.069039 restraints weight = 61445.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069995 restraints weight = 49821.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.070516 restraints weight = 38971.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071114 restraints weight = 35057.246| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 33159 Z= 0.179 Angle : 0.718 10.437 45372 Z= 0.342 Chirality : 0.046 0.289 5445 Planarity : 0.004 0.055 5490 Dihedral : 9.414 76.111 7339 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.93 % Allowed : 21.08 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.13), residues: 3801 helix: -1.30 (0.25), residues: 384 sheet: -0.96 (0.15), residues: 1245 loop : -1.76 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 38 TYR 0.020 0.001 TYR A 59 PHE 0.024 0.002 PHE q 91 TRP 0.031 0.001 TRP M 36 HIS 0.004 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00411 (32946) covalent geometry : angle 0.68843 (44790) SS BOND : bond 0.00300 ( 57) SS BOND : angle 1.38345 ( 114) hydrogen bonds : bond 0.03160 ( 870) hydrogen bonds : angle 4.96310 ( 2214) link_ALPHA1-2 : bond 0.00422 ( 3) link_ALPHA1-2 : angle 1.67927 ( 9) link_ALPHA1-3 : bond 0.01017 ( 15) link_ALPHA1-3 : angle 1.65690 ( 45) link_ALPHA1-6 : bond 0.00566 ( 12) link_ALPHA1-6 : angle 1.77359 ( 36) link_BETA1-4 : bond 0.00470 ( 69) link_BETA1-4 : angle 1.62537 ( 207) link_NAG-ASN : bond 0.00446 ( 57) link_NAG-ASN : angle 2.55379 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 280 time to evaluate : 1.346 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: G 161 MET cc_start: 0.7746 (tpp) cc_final: 0.7369 (ttm) REVERT: G 271 MET cc_start: 0.7669 (mtt) cc_final: 0.7310 (mtt) REVERT: G 272 ILE cc_start: 0.8933 (pt) cc_final: 0.8649 (mt) REVERT: G 482 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7374 (mm-30) REVERT: H 32 PHE cc_start: 0.6386 (m-80) cc_final: 0.5632 (m-10) REVERT: L 6 GLN cc_start: 0.0868 (OUTLIER) cc_final: -0.0502 (mm110) REVERT: m 30 ARG cc_start: 0.9001 (mtp-110) cc_final: 0.8649 (mmm-85) REVERT: m 43 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8915 (mtpt) REVERT: m 53 ASP cc_start: 0.8472 (p0) cc_final: 0.8180 (p0) REVERT: E 33 ASN cc_start: 0.8063 (p0) cc_final: 0.7817 (p0) REVERT: E 95 MET cc_start: 0.8389 (ptm) cc_final: 0.7806 (ttp) REVERT: C 6 GLN cc_start: 0.1315 (OUTLIER) cc_final: 0.0398 (mm-40) REVERT: F 16 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7228 (tm-30) REVERT: F 30 ARG cc_start: 0.8946 (ttp-110) cc_final: 0.8253 (tpp80) REVERT: F 103 LYS cc_start: 0.8559 (mmmm) cc_final: 0.8229 (mppt) REVERT: J 100 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7785 (t80) REVERT: K 1 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: K 98 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7601 (tm-30) REVERT: P 95 MET cc_start: 0.8334 (ptm) cc_final: 0.8044 (ttp) REVERT: M 59 TYR cc_start: 0.5681 (m-80) cc_final: 0.5017 (m-10) REVERT: N 4 MET cc_start: -0.2271 (mtp) cc_final: -0.2507 (mtp) REVERT: N 6 GLN cc_start: 0.0628 (OUTLIER) cc_final: 0.0189 (mm-40) REVERT: Q 32 ASN cc_start: 0.8320 (m-40) cc_final: 0.7787 (m-40) REVERT: Q 43 LYS cc_start: 0.9266 (mmmm) cc_final: 0.8904 (mtpt) REVERT: S 99 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8269 (p0) REVERT: S 100 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7848 (t80) REVERT: T 32 MET cc_start: 0.8208 (tpt) cc_final: 0.7156 (tpp) outliers start: 98 outliers final: 81 residues processed: 359 average time/residue: 0.2107 time to fit residues: 121.5635 Evaluate side-chains 356 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 267 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 18 VAL Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain K residue 1 GLU Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 101 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 358 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 320 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 334 optimal weight: 0.0570 chunk 146 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN F 1 GLN I 51 ASN P 33 ASN M 53 ASN R 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.107757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073076 restraints weight = 80491.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.070734 restraints weight = 59729.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.071648 restraints weight = 48816.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.072523 restraints weight = 37929.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.072557 restraints weight = 33492.082| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33159 Z= 0.122 Angle : 0.692 10.409 45372 Z= 0.331 Chirality : 0.045 0.276 5445 Planarity : 0.004 0.057 5490 Dihedral : 9.107 73.402 7339 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.54 % Allowed : 21.61 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.13), residues: 3801 helix: -1.48 (0.24), residues: 420 sheet: -0.71 (0.15), residues: 1170 loop : -1.74 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.020 0.001 TYR A 59 PHE 0.020 0.001 PHE q 91 TRP 0.029 0.001 TRP M 34 HIS 0.004 0.001 HIS F 3 Details of bonding type rmsd covalent geometry : bond 0.00277 (32946) covalent geometry : angle 0.66633 (44790) SS BOND : bond 0.00244 ( 57) SS BOND : angle 1.23895 ( 114) hydrogen bonds : bond 0.02957 ( 870) hydrogen bonds : angle 4.78290 ( 2214) link_ALPHA1-2 : bond 0.00512 ( 3) link_ALPHA1-2 : angle 1.46982 ( 9) link_ALPHA1-3 : bond 0.01124 ( 15) link_ALPHA1-3 : angle 1.58454 ( 45) link_ALPHA1-6 : bond 0.00616 ( 12) link_ALPHA1-6 : angle 1.68984 ( 36) link_BETA1-4 : bond 0.00469 ( 69) link_BETA1-4 : angle 1.54620 ( 207) link_NAG-ASN : bond 0.00300 ( 57) link_NAG-ASN : angle 2.34844 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7602 Ramachandran restraints generated. 3801 Oldfield, 0 Emsley, 3801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 303 time to evaluate : 1.299 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: G 161 MET cc_start: 0.7755 (tpp) cc_final: 0.7382 (ttm) REVERT: G 272 ILE cc_start: 0.8889 (pt) cc_final: 0.8610 (mt) REVERT: G 482 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: H 4 LEU cc_start: 0.7233 (pt) cc_final: 0.6998 (pp) REVERT: H 32 PHE cc_start: 0.6348 (m-80) cc_final: 0.5628 (m-10) REVERT: L 6 GLN cc_start: 0.1189 (OUTLIER) cc_final: -0.0263 (mm110) REVERT: m 16 GLU cc_start: 0.7403 (pp20) cc_final: 0.6568 (tm-30) REVERT: m 30 ARG cc_start: 0.9032 (mtp-110) cc_final: 0.8684 (mmm-85) REVERT: m 43 LYS cc_start: 0.9207 (mmmm) cc_final: 0.8899 (mtpt) REVERT: m 53 ASP cc_start: 0.8432 (p0) cc_final: 0.8151 (p0) REVERT: E 33 ASN cc_start: 0.8019 (p0) cc_final: 0.7766 (p0) REVERT: E 95 MET cc_start: 0.8317 (ptm) cc_final: 0.7737 (ttp) REVERT: C 6 GLN cc_start: 0.1608 (OUTLIER) cc_final: 0.0597 (mm-40) REVERT: F 16 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7255 (tm-30) REVERT: F 30 ARG cc_start: 0.8933 (ttp-110) cc_final: 0.8233 (tpp80) REVERT: F 103 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8211 (mppt) REVERT: J 100 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7760 (t80) REVERT: K 98 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7580 (tm-30) REVERT: D 657 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8231 (pp20) REVERT: P 95 MET cc_start: 0.8249 (ptm) cc_final: 0.7924 (ttm) REVERT: P 302 ASN cc_start: 0.8684 (t0) cc_final: 0.8393 (t0) REVERT: M 53 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7443 (p0) REVERT: M 59 TYR cc_start: 0.5680 (m-80) cc_final: 0.5007 (m-10) REVERT: N 6 GLN cc_start: 0.1173 (OUTLIER) cc_final: 0.0611 (mm-40) REVERT: Q 32 ASN cc_start: 0.8243 (m-40) cc_final: 0.7791 (m-40) REVERT: Q 43 LYS cc_start: 0.9258 (mmmm) cc_final: 0.8865 (mtpt) REVERT: S 99 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8113 (p0) REVERT: S 100 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7857 (t80) REVERT: T 32 MET cc_start: 0.8066 (tpt) cc_final: 0.7037 (tpp) outliers start: 85 outliers final: 72 residues processed: 371 average time/residue: 0.2091 time to fit residues: 124.8508 Evaluate side-chains 359 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 279 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 139 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 423 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 482 GLU Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain m residue 2 VAL Chi-restraints excluded: chain m residue 70 SER Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 58 ILE Chi-restraints excluded: chain n residue 105 ILE Chi-restraints excluded: chain q residue 13 THR Chi-restraints excluded: chain q residue 51 ILE Chi-restraints excluded: chain q residue 99 ASP Chi-restraints excluded: chain r residue 51 SER Chi-restraints excluded: chain r residue 73 THR Chi-restraints excluded: chain r residue 74 ILE Chi-restraints excluded: chain O residue 573 ILE Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 100 TYR Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain K residue 42 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 126 CYS Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 208 VAL Chi-restraints excluded: chain P residue 236 THR Chi-restraints excluded: chain P residue 320 THR Chi-restraints excluded: chain P residue 423 ILE Chi-restraints excluded: chain P residue 467 THR Chi-restraints excluded: chain P residue 488 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 53 ASN Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 85 VAL Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 70 SER Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 TYR Chi-restraints excluded: chain S residue 100 CYS Chi-restraints excluded: chain T residue 42 VAL Chi-restraints excluded: chain T residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 314 optimal weight: 30.0000 chunk 241 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 374 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 377 optimal weight: 0.6980 chunk 187 optimal weight: 50.0000 chunk 172 optimal weight: 0.0870 chunk 270 optimal weight: 0.0870 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 1 GLN F 32 ASN I 51 ASN P 33 ASN M 53 ASN R 51 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.107804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.073782 restraints weight = 80425.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.071181 restraints weight = 58433.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.072331 restraints weight = 49343.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072496 restraints weight = 41458.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072879 restraints weight = 35162.671| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.297 33159 Z= 0.198 Angle : 0.806 59.153 45372 Z= 0.426 Chirality : 0.050 1.130 5445 Planarity : 0.005 0.192 5490 Dihedral : 9.112 73.418 7339 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.21 % Favored : 93.76 % Rotamer: Outliers : 2.57 % Allowed : 22.03 % Favored : 75.40 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.13), residues: 3801 helix: -1.47 (0.24), residues: 420 sheet: -0.83 (0.15), residues: 1230 loop : -1.69 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG A 105 TYR 0.027 0.001 TYR n 87 PHE 0.044 0.001 PHE J 91 TRP 0.025 0.001 TRP M 34 HIS 0.004 0.001 HIS Q 3 Details of bonding type rmsd covalent geometry : bond 0.00410 (32946) covalent geometry : angle 0.77951 (44790) SS BOND : bond 0.00250 ( 57) SS BOND : angle 1.22473 ( 114) hydrogen bonds : bond 0.02968 ( 870) hydrogen bonds : angle 4.78149 ( 2214) link_ALPHA1-2 : bond 0.00509 ( 3) link_ALPHA1-2 : angle 1.47295 ( 9) link_ALPHA1-3 : bond 0.01008 ( 15) link_ALPHA1-3 : angle 1.56911 ( 45) link_ALPHA1-6 : bond 0.00615 ( 12) link_ALPHA1-6 : angle 1.68680 ( 36) link_BETA1-4 : bond 0.00473 ( 69) link_BETA1-4 : angle 1.54390 ( 207) link_NAG-ASN : bond 0.00575 ( 57) link_NAG-ASN : angle 2.78956 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6154.72 seconds wall clock time: 107 minutes 15.57 seconds (6435.57 seconds total)