Starting phenix.real_space_refine on Fri Mar 6 01:30:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pc2_13316/03_2026/7pc2_13316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pc2_13316/03_2026/7pc2_13316.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pc2_13316/03_2026/7pc2_13316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pc2_13316/03_2026/7pc2_13316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pc2_13316/03_2026/7pc2_13316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pc2_13316/03_2026/7pc2_13316.map" } resolution = 2.8 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= 0.049 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 156 5.16 5 C 16839 2.51 5 N 4398 2.21 5 O 5670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s 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: 27063 Number of models: 1 Model: "" Number of chains: 68 Chain: "O" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1031 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "P" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1031 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "N" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1031 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "R" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 821 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3499 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3499 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 4 Chain: "C" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3499 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "D" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "F" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1024 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "K" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "G" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "J" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "b" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 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: "l" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "m" 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: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "r" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "t" 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: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "z" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "0" 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: "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: 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: "3" 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: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "6" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "8" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "9" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.42, per 1000 atoms: 0.24 Number of scatterers: 27063 At special positions: 0 Unit cell: (182.75, 173.4, 123.25, 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 156 16.00 O 5670 8.00 N 4398 7.00 C 16839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 105 " - pdb=" SG CYS O 110 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 105 " - pdb=" SG CYS Q 110 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=1.74 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.36 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.42 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.72 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=1.94 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.94 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.56 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 5 5 " - " MAN 5 6 " " MAN 5 7 " - " MAN 5 8 " " MAN 6 4 " - " MAN 6 5 " " MAN 6 5 " - " MAN 6 6 " " MAN 6 8 " - " MAN 6 9 " " MAN 6 10 " - " MAN 6 11 " " MAN W 5 " - " MAN W 6 " " MAN W 8 " - " MAN W 9 " " MAN X 4 " - " MAN X 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " " MAN a 10 " - " MAN a 11 " " MAN b 5 " - " MAN b 6 " " MAN l 4 " - " MAN l 5 " " MAN q 5 " - " MAN q 6 " " MAN q 7 " - " MAN q 8 " " MAN r 4 " - " MAN r 5 " " MAN r 5 " - " MAN r 6 " " MAN r 8 " - " MAN r 9 " " MAN r 10 " - " MAN r 11 " " MAN s 5 " - " MAN s 6 " " MAN s 8 " - " MAN s 9 " " MAN y 5 " - " MAN y 6 " " MAN y 8 " - " MAN y 9 " " MAN z 4 " - " MAN z 5 " ALPHA1-3 " BMA 1 3 " - " MAN 1 4 " " BMA 5 3 " - " MAN 5 7 " " MAN 5 4 " - " MAN 5 5 " " BMA 6 3 " - " MAN 6 4 " " MAN 6 7 " - " MAN 6 8 " " BMA W 3 " - " MAN W 8 " " MAN W 4 " - " MAN W 7 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 8 " " BMA b 3 " - " MAN b 7 " " MAN b 4 " - " MAN b 5 " " BMA e 3 " - " MAN e 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA n 3 " - " MAN n 4 " " BMA q 3 " - " MAN q 7 " " MAN q 4 " - " MAN q 5 " " BMA r 3 " - " MAN r 4 " " MAN r 7 " - " MAN r 8 " " BMA s 3 " - " MAN s 8 " " MAN s 4 " - " MAN s 7 " " BMA y 3 " - " MAN y 8 " " MAN y 4 " - " MAN y 7 " " BMA z 3 " - " MAN z 4 " " MAN z 6 " - " MAN z 7 " ALPHA1-6 " BMA 1 3 " - " MAN 1 5 " " BMA 5 3 " - " MAN 5 4 " " BMA 6 3 " - " MAN 6 7 " " MAN 6 7 " - " MAN 6 10 " " BMA W 3 " - " MAN W 4 " " MAN W 4 " - " MAN W 5 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 10 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 5 " " BMA l 3 " - " MAN l 6 " " MAN l 6 " - " MAN l 8 " " BMA n 3 " - " MAN n 5 " " BMA q 3 " - " MAN q 4 " " BMA r 3 " - " MAN r 7 " " MAN r 7 " - " MAN r 10 " " BMA s 3 " - " MAN s 4 " " MAN s 4 " - " MAN s 5 " " BMA y 3 " - " MAN y 4 " " MAN y 4 " - " MAN y 5 " " BMA z 3 " - " MAN z 6 " " MAN z 6 " - " MAN z 8 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 5 2 " - " BMA 5 3 " " NAG 6 1 " - " NAG 6 2 " " NAG 6 2 " - " BMA 6 3 " " NAG 7 1 " - " NAG 7 2 " " NAG 8 1 " - " NAG 8 2 " " NAG 9 1 " - " NAG 9 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG 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 h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN C 301 " " NAG 1 1 " - " ASN C 363 " " NAG 2 1 " - " ASN C 386 " " NAG 3 1 " - " ASN C 392 " " NAG 4 1 " - " ASN C 448 " " NAG 5 1 " - " ASN C 295 " " NAG 6 1 " - " ASN C 332 " " NAG 7 1 " - " ASN L 72 " " NAG 8 1 " - " ASN H 72 " " NAG 9 1 " - " ASN J 72 " " NAG A 601 " - " ASN A 339 " " NAG A 602 " - " ASN A 355 " " NAG A 603 " - " ASN A 411 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 234 " " NAG B 601 " - " ASN B 234 " " NAG B 602 " - " ASN B 355 " " NAG B 603 " - " ASN B 339 " " NAG B 604 " - " ASN B 411 " " NAG B 605 " - " ASN B 137 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 339 " " NAG C 604 " - " ASN C 411 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 637 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN A 133 " " NAG U 1 " - " ASN A 156 " " NAG V 1 " - " ASN A 160 " " NAG W 1 " - " ASN A 262 " " NAG X 1 " - " ASN A 276 " " NAG Y 1 " - " ASN A 301 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 332 " " NAG b 1 " - " ASN A 295 " " NAG c 1 " - " ASN A 392 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 363 " " NAG f 1 " - " ASN A 386 " " NAG g 1 " - " ASN B 88 " " NAG h 1 " - " ASN B 133 " " NAG i 1 " - " ASN B 156 " " NAG j 1 " - " ASN B 160 " " NAG k 1 " - " ASN B 197 " " NAG l 1 " - " ASN B 276 " " NAG m 1 " - " ASN B 301 " " NAG n 1 " - " ASN B 363 " " NAG o 1 " - " ASN B 386 " " NAG p 1 " - " ASN B 448 " " NAG q 1 " - " ASN B 295 " " NAG r 1 " - " ASN B 332 " " NAG s 1 " - " ASN B 262 " " NAG t 1 " - " ASN B 392 " " NAG u 1 " - " ASN C 88 " " NAG v 1 " - " ASN C 156 " " NAG w 1 " - " ASN C 160 " " NAG x 1 " - " ASN C 197 " " NAG y 1 " - " ASN C 262 " " NAG z 1 " - " ASN C 276 " Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.0 seconds 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5700 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 57 sheets defined 15.4% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'O' and resid 111 through 116 removed outlier: 3.568A pdb=" N TYR O 116 " --> pdb=" O TRP O 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.813A pdb=" N PHE P 83 " --> pdb=" O SER P 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 116 removed outlier: 3.548A pdb=" N TYR M 116 " --> pdb=" O TRP M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.895A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 116 removed outlier: 3.533A pdb=" N TYR Q 116 " --> pdb=" O TRP Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.848A pdb=" N PHE R 83 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.235A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.587A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.567A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.695A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.596A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 115 removed outlier: 4.214A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.523A pdb=" N CYS B 126 " --> pdb=" O THR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 352 removed outlier: 3.584A pdb=" N VAL B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN B 348 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.634A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.615A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.721A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.576A pdb=" N VAL C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.578A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.904A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.660A pdb=" N VAL D 580 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 627 through 634 removed outlier: 3.819A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 removed outlier: 3.546A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 645 " --> pdb=" O ILE D 641 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.601A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 527 Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 543 removed outlier: 4.011A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 removed outlier: 3.933A pdb=" N LEU E 576 " --> pdb=" O GLY E 572 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 581 " --> pdb=" O GLN E 577 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP E 589 " --> pdb=" O ARG E 585 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 619 through 624 Processing helix chain 'E' and resid 627 through 634 removed outlier: 3.823A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.508A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 662 removed outlier: 3.836A pdb=" N ASN E 656 " --> pdb=" O GLN E 652 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU E 657 " --> pdb=" O GLN E 653 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP E 659 " --> pdb=" O LYS E 655 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.906A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.970A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU F 581 " --> pdb=" O GLN F 577 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 627 through 634 removed outlier: 3.677A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 removed outlier: 3.612A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 663 removed outlier: 3.612A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.687A pdb=" N TYR K 32 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 64 removed outlier: 3.674A pdb=" N GLN K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.549A pdb=" N ASP G 31 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.709A pdb=" N GLN G 64 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.750A pdb=" N TYR I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'O' and resid 58 through 60 removed outlier: 5.065A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.834A pdb=" N SER P 7 " --> pdb=" O SER P 22 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER P 22 " --> pdb=" O SER P 7 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER P 67 " --> pdb=" O GLU P 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 45 through 48 removed outlier: 6.584A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'M' and resid 58 through 60 removed outlier: 5.093A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.849A pdb=" N SER N 7 " --> pdb=" O SER N 22 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER N 67 " --> pdb=" O GLU N 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.523A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN N 92 " --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG N 96 " --> pdb=" O ASN N 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.523A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'Q' and resid 58 through 60 removed outlier: 5.157A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.657A pdb=" N SER R 7 " --> pdb=" O SER R 22 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER R 22 " --> pdb=" O SER R 7 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU R 70 " --> pdb=" O SER R 67 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 67 " --> pdb=" O GLU R 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.558A pdb=" N LEU R 11 " --> pdb=" O GLU R 106 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.292A pdb=" N VAL D 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N VAL A 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR D 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N TYR A 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N CYS D 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.872A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.668A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AB9, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AC1, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC2, first strand: chain 'A' and resid 200 through 202 removed outlier: 6.447A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.004A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.633A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AC6, first strand: chain 'B' and resid 494 through 499 removed outlier: 5.245A pdb=" N VAL F 608 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL B 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR F 606 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N TYR B 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N CYS F 604 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.881A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.728A pdb=" N VAL B 75 " --> pdb=" O CYS B 54 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AD1, first strand: chain 'B' and resid 130 through 133 Processing sheet with id=AD2, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'B' and resid 259 through 261 removed outlier: 5.965A pdb=" N LEU B 260 " --> pdb=" O THR B 450 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N GLY B 441 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASN B 300 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 443 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER B 334 " --> pdb=" O GLN B 293 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 330 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 421 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 376 " --> pdb=" O PHE B 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 271 through 273 removed outlier: 3.730A pdb=" N SER B 393 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AD6, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.233A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.863A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.730A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AE1, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AE2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE3, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.994A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.609A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AE6, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE7, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.518A pdb=" N THR K 110 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.518A pdb=" N THR K 110 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.567A pdb=" N THR G 110 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TRP G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.567A pdb=" N THR G 110 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 18 through 24 Processing sheet with id=AF3, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.571A pdb=" N THR I 110 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.571A pdb=" N THR I 110 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.542A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.771A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.728A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 45 through 48 removed outlier: 6.787A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.636A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 10 through 11 799 hydrogen bonds defined for protein. 2007 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.52: 23853 1.52 - 1.89: 3753 1.89 - 2.25: 0 2.25 - 2.62: 0 2.62 - 2.98: 11 Bond restraints: 27617 Sorted by residual: bond pdb=" C GLY H 27 " pdb=" N TYR H 32 " ideal model delta sigma weight residual 1.330 2.981 -1.651 1.30e-02 5.92e+03 1.61e+04 bond pdb=" C GLY L 27 " pdb=" N TYR L 32 " ideal model delta sigma weight residual 1.330 2.915 -1.585 1.30e-02 5.92e+03 1.49e+04 bond pdb=" C TYR L 91 " pdb=" N GLU L 96 " ideal model delta sigma weight residual 1.332 2.895 -1.563 1.29e-02 6.01e+03 1.47e+04 bond pdb=" C ASP C 141 " pdb=" N MET C 150 " ideal model delta sigma weight residual 1.333 2.930 -1.597 1.36e-02 5.41e+03 1.38e+04 bond pdb=" C GLY J 27 " pdb=" N TYR J 32 " ideal model delta sigma weight residual 1.330 2.925 -1.596 1.38e-02 5.25e+03 1.34e+04 ... (remaining 27612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.67: 37478 16.67 - 33.34: 14 33.34 - 50.01: 1 50.01 - 66.68: 1 66.68 - 83.35: 9 Bond angle restraints: 37503 Sorted by residual: angle pdb=" O GLY J 27 " pdb=" C GLY J 27 " pdb=" N TYR J 32 " ideal model delta sigma weight residual 122.60 46.07 76.53 1.07e+00 8.73e-01 5.12e+03 angle pdb=" O GLY H 27 " pdb=" C GLY H 27 " pdb=" N TYR H 32 " ideal model delta sigma weight residual 122.96 41.61 81.35 1.22e+00 6.72e-01 4.45e+03 angle pdb=" O GLY L 27 " pdb=" C GLY L 27 " pdb=" N TYR L 32 " ideal model delta sigma weight residual 122.95 48.05 74.90 1.15e+00 7.56e-01 4.24e+03 angle pdb=" O TYR J 91 " pdb=" C TYR J 91 " pdb=" N GLU J 96 " ideal model delta sigma weight residual 122.59 39.24 83.35 1.33e+00 5.65e-01 3.93e+03 angle pdb=" O TYR H 91 " pdb=" C TYR H 91 " pdb=" N GLU H 96 " ideal model delta sigma weight residual 122.59 45.81 76.78 1.33e+00 5.65e-01 3.33e+03 ... (remaining 37498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.61: 17469 24.61 - 49.22: 1067 49.22 - 73.83: 249 73.83 - 98.44: 175 98.44 - 123.05: 104 Dihedral angle restraints: 19064 sinusoidal: 10176 harmonic: 8888 Sorted by residual: dihedral pdb=" CB CYS B 218 " pdb=" SG CYS B 218 " pdb=" SG CYS B 247 " pdb=" CB CYS B 247 " ideal model delta sinusoidal sigma weight residual 93.00 168.04 -75.04 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CB CYS Q 105 " pdb=" SG CYS Q 105 " pdb=" SG CYS Q 110 " pdb=" CB CYS Q 110 " ideal model delta sinusoidal sigma weight residual -86.00 -15.12 -70.88 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 22.99 70.01 1 1.00e+01 1.00e-02 6.32e+01 ... (remaining 19061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 4688 0.172 - 0.345: 55 0.345 - 0.517: 5 0.517 - 0.690: 0 0.690 - 0.862: 1 Chirality restraints: 4749 Sorted by residual: chirality pdb=" CA SER H 7 " pdb=" N SER H 7 " pdb=" C SER H 7 " pdb=" CB SER H 7 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 411 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" CA SER M 108 " pdb=" N SER M 108 " pdb=" C SER M 108 " pdb=" CB SER M 108 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.85e+00 ... (remaining 4746 not shown) Planarity restraints: 4545 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY H 27 " -0.202 2.00e-02 2.50e+03 2.71e-01 7.35e+02 pdb=" C GLY H 27 " 0.448 2.00e-02 2.50e+03 pdb=" O GLY H 27 " -0.229 2.00e-02 2.50e+03 pdb=" N TYR H 32 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 141 " 0.175 2.00e-02 2.50e+03 2.63e-01 6.89e+02 pdb=" C ASP C 141 " -0.414 2.00e-02 2.50e+03 pdb=" O ASP C 141 " 0.269 2.00e-02 2.50e+03 pdb=" N MET C 150 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 91 " 0.169 2.00e-02 2.50e+03 2.50e-01 6.24e+02 pdb=" C TYR L 91 " -0.417 2.00e-02 2.50e+03 pdb=" O TYR L 91 " 0.214 2.00e-02 2.50e+03 pdb=" N GLU L 96 " 0.034 2.00e-02 2.50e+03 ... (remaining 4542 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 120 2.43 - 3.05: 17279 3.05 - 3.66: 35564 3.66 - 4.28: 56675 4.28 - 4.90: 95883 Nonbonded interactions: 205521 Sorted by model distance: nonbonded pdb=" OD1 ASP M 104 " pdb=" N CYS M 105 " model vdw 1.809 3.120 nonbonded pdb=" CA CYS B 218 " pdb=" SG CYS B 247 " model vdw 1.853 3.064 nonbonded pdb=" O SER H 7 " pdb=" OG SER H 7 " model vdw 2.010 3.040 nonbonded pdb=" OD1 ASP M 120 " pdb=" N VAL M 121 " model vdw 2.043 3.120 nonbonded pdb=" O SER Q 108 " pdb=" O6 NAG b 1 " model vdw 2.098 3.040 ... (remaining 205516 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain '3' selection = chain 'Y' selection = chain 'c' selection = chain 'f' selection = chain 'm' selection = chain 'o' selection = chain 't' selection = chain 'u' } ncs_group { reference = chain '1' selection = chain 'e' selection = chain 'n' } ncs_group { reference = chain '4' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'p' selection = chain 'v' selection = chain 'w' selection = chain 'x' } ncs_group { reference = (chain '5' and resid 5 through 8) selection = (chain 'W' and resid 6 through 9) selection = (chain 'X' and resid 5 through 8) selection = (chain 'b' and resid 4 through 7) selection = (chain 'l' and resid 5 through 8) selection = (chain 'q' and resid 5 through 8) selection = (chain 's' and resid 6 through 9) selection = (chain 'y' and resid 6 through 9) selection = (chain 'z' and resid 5 through 8) } ncs_group { reference = chain '6' selection = chain 'a' selection = chain 'r' } ncs_group { reference = (chain 'A' and resid 32 through 604) selection = (chain 'B' and resid 32 through 604) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.010 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0637 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 : 0.034 1.651 27874 Z= 2.335 Angle : 1.753 83.352 38227 Z= 1.161 Chirality : 0.060 0.862 4749 Planarity : 0.013 0.271 4481 Dihedral : 19.871 123.049 13223 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.49 % Allowed : 19.55 % Favored : 78.96 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 4.88 % 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: -3.81 (0.13), residues: 3009 helix: -4.00 (0.14), residues: 381 sheet: -1.46 (0.15), residues: 1014 loop : -2.94 (0.13), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 166 TYR 0.016 0.001 TYR O 95 PHE 0.011 0.002 PHE O 27 TRP 0.045 0.002 TRP B 69 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.03313 (27617) covalent geometry : angle 1.65859 (37503) SS BOND : bond 0.20221 ( 47) SS BOND : angle 10.39840 ( 94) hydrogen bonds : bond 0.24173 ( 772) hydrogen bonds : angle 8.14022 ( 2007) link_ALPHA1-2 : bond 0.00220 ( 26) link_ALPHA1-2 : angle 2.20964 ( 78) link_ALPHA1-3 : bond 0.00347 ( 27) link_ALPHA1-3 : angle 2.29227 ( 81) link_ALPHA1-6 : bond 0.00419 ( 24) link_ALPHA1-6 : angle 1.94271 ( 72) link_BETA1-4 : bond 0.00529 ( 69) link_BETA1-4 : angle 2.50715 ( 207) link_NAG-ASN : bond 0.01074 ( 64) link_NAG-ASN : angle 3.03442 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6018 Ramachandran restraints generated. 3009 Oldfield, 0 Emsley, 3009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 496 time to evaluate : 0.931 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: O 2 MET cc_start: 0.5710 (ttp) cc_final: 0.4900 (mtt) REVERT: O 70 ILE cc_start: 0.2509 (tt) cc_final: 0.1766 (tp) REVERT: P 69 THR cc_start: 0.6625 (t) cc_final: 0.6255 (m) REVERT: M 79 LEU cc_start: 0.2598 (tp) cc_final: 0.1946 (tp) REVERT: Q 50 TYR cc_start: -0.0101 (t80) cc_final: -0.1011 (t80) REVERT: R 42 GLN cc_start: 0.2794 (tt0) cc_final: 0.2568 (tp40) REVERT: A 100 MET cc_start: 0.0557 (mtp) cc_final: -0.0766 (tpt) REVERT: A 298 ARG cc_start: 0.2990 (tmm-80) cc_final: 0.2539 (tpp-160) REVERT: A 386 ASN cc_start: 0.2834 (t0) cc_final: 0.2611 (m-40) REVERT: A 412 ASP cc_start: 0.2372 (OUTLIER) cc_final: 0.1903 (t0) REVERT: C 109 ILE cc_start: -0.0275 (mt) cc_final: -0.0924 (pt) REVERT: C 286 VAL cc_start: 0.3933 (t) cc_final: 0.3489 (t) REVERT: E 550 GLN cc_start: 0.3175 (OUTLIER) cc_final: 0.2793 (mm110) REVERT: K 6 GLN cc_start: -0.2001 (tt0) cc_final: -0.2316 (pm20) REVERT: G 76 TYR cc_start: 0.2674 (m-80) cc_final: 0.2426 (m-80) REVERT: L 42 LYS cc_start: 0.3382 (mmtm) cc_final: 0.2790 (pptt) outliers start: 40 outliers final: 4 residues processed: 527 average time/residue: 0.6176 time to fit residues: 377.4191 Evaluate side-chains 252 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 246 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain H residue 66 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN O 74 ASN ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN P 42 GLN M 3 GLN M 80 HIS ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN N 79 GLN N 92 ASN Q 74 ASN R 32 ASN R 42 GLN R 92 ASN A 67 ASN A 99 ASN A 183 GLN A 185 ASN A 249 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 289 ASN A 293 GLN A 462 ASN B 183 GLN B 185 ASN B 293 GLN B 377 ASN B 432 GLN C 33 ASN C 72 HIS C 185 ASN C 249 HIS C 280 ASN C 293 GLN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 ASN E 650 GLN E 658 GLN F 651 ASN F 652 GLN K 3 GLN I 6 GLN H 3 GLN H 6 GLN H 34 ASN J 79 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.126216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.096615 restraints weight = 58439.088| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.39 r_work: 0.3410 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1180 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 27874 Z= 0.178 Angle : 0.919 14.083 38227 Z= 0.432 Chirality : 0.053 0.684 4749 Planarity : 0.005 0.078 4481 Dihedral : 15.091 108.455 7575 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.47 % Allowed : 21.94 % Favored : 72.59 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.88 % 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: -2.72 (0.14), residues: 3031 helix: -2.35 (0.22), residues: 405 sheet: -0.83 (0.16), residues: 1044 loop : -2.38 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 38 TYR 0.020 0.002 TYR P 89 PHE 0.035 0.002 PHE A 159 TRP 0.036 0.002 TRP N 94 HIS 0.018 0.002 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00379 (27617) covalent geometry : angle 0.86775 (37503) SS BOND : bond 0.00581 ( 47) SS BOND : angle 1.86808 ( 94) hydrogen bonds : bond 0.04979 ( 772) hydrogen bonds : angle 5.95393 ( 2007) link_ALPHA1-2 : bond 0.00646 ( 26) link_ALPHA1-2 : angle 2.12253 ( 78) link_ALPHA1-3 : bond 0.00986 ( 27) link_ALPHA1-3 : angle 1.92505 ( 81) link_ALPHA1-6 : bond 0.00880 ( 24) link_ALPHA1-6 : angle 1.92810 ( 72) link_BETA1-4 : bond 0.00677 ( 69) link_BETA1-4 : angle 2.36128 ( 207) link_NAG-ASN : bond 0.01157 ( 64) link_NAG-ASN : angle 2.92307 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 301 time to evaluate : 0.845 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: P 99 PHE cc_start: 0.3233 (OUTLIER) cc_final: 0.3027 (m-10) REVERT: M 20 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4931 (tt) REVERT: M 79 LEU cc_start: 0.2994 (tp) cc_final: 0.2743 (tp) REVERT: M 81 LEU cc_start: -0.0866 (OUTLIER) cc_final: -0.1133 (tm) REVERT: M 83 MET cc_start: 0.1730 (OUTLIER) cc_final: 0.1180 (tpt) REVERT: N 4 MET cc_start: 0.5742 (mpp) cc_final: 0.4665 (tpp) REVERT: N 108 LYS cc_start: -0.5205 (OUTLIER) cc_final: -0.5445 (tttm) REVERT: Q 83 MET cc_start: 0.4308 (pmm) cc_final: 0.2368 (tpt) REVERT: R 42 GLN cc_start: 0.3151 (tt0) cc_final: 0.2743 (tp40) REVERT: A 100 MET cc_start: -0.0170 (mtp) cc_final: -0.0686 (tpt) REVERT: A 166 ARG cc_start: -0.2812 (OUTLIER) cc_final: -0.4492 (tpt90) REVERT: A 205 CYS cc_start: -0.1443 (OUTLIER) cc_final: -0.2281 (t) REVERT: A 298 ARG cc_start: 0.3304 (tmm-80) cc_final: 0.3046 (ttt180) REVERT: A 341 THR cc_start: 0.0355 (p) cc_final: -0.1984 (m) REVERT: A 426 MET cc_start: 0.0146 (pmm) cc_final: -0.1755 (mpt) REVERT: B 96 TRP cc_start: 0.4663 (m-90) cc_final: 0.3876 (m100) REVERT: C 258 GLN cc_start: 0.3059 (OUTLIER) cc_final: 0.2537 (tp40) REVERT: C 335 LYS cc_start: 0.1546 (OUTLIER) cc_final: 0.1319 (tptt) REVERT: D 537 LEU cc_start: 0.3151 (OUTLIER) cc_final: 0.2287 (tt) REVERT: E 550 GLN cc_start: 0.3101 (OUTLIER) cc_final: 0.2528 (mt0) REVERT: K 6 GLN cc_start: -0.1654 (tt0) cc_final: -0.2346 (pm20) REVERT: K 80 MET cc_start: 0.1079 (ptt) cc_final: 0.0458 (ttm) REVERT: G 51 ILE cc_start: 0.0459 (tt) cc_final: -0.0252 (mm) REVERT: I 100 TRP cc_start: 0.2080 (m100) cc_final: -0.1347 (p90) REVERT: L 42 LYS cc_start: 0.3571 (mmtm) cc_final: 0.3074 (pttp) REVERT: H 45 LYS cc_start: 0.3771 (OUTLIER) cc_final: 0.3381 (ptpp) outliers start: 147 outliers final: 37 residues processed: 411 average time/residue: 0.5016 time to fit residues: 247.4921 Evaluate side-chains 266 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 99 PHE Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 108 LYS Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 335 LYS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 164 optimal weight: 0.0040 chunk 34 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN A 374 HIS B 99 ASN B 356 ASN C 258 GLN C 352 HIS D 590 GLN F 540 GLN F 543 ASN G 62 GLN J 79 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.131429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.102802 restraints weight = 59259.013| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.44 r_work: 0.3521 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1501 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 27874 Z= 0.162 Angle : 0.844 12.525 38227 Z= 0.393 Chirality : 0.051 0.555 4749 Planarity : 0.005 0.065 4481 Dihedral : 12.426 103.684 7566 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.67 % Favored : 94.29 % Rotamer: Outliers : 5.14 % Allowed : 24.25 % Favored : 70.61 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.88 % 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: -1.96 (0.14), residues: 3031 helix: -1.37 (0.24), residues: 408 sheet: -0.29 (0.16), residues: 978 loop : -1.96 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Q 67 TYR 0.025 0.002 TYR O 50 PHE 0.022 0.002 PHE A 159 TRP 0.028 0.002 TRP Q 36 HIS 0.015 0.002 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00342 (27617) covalent geometry : angle 0.79464 (37503) SS BOND : bond 0.00477 ( 47) SS BOND : angle 1.64006 ( 94) hydrogen bonds : bond 0.04245 ( 772) hydrogen bonds : angle 5.54872 ( 2007) link_ALPHA1-2 : bond 0.00592 ( 26) link_ALPHA1-2 : angle 1.91764 ( 78) link_ALPHA1-3 : bond 0.01047 ( 27) link_ALPHA1-3 : angle 1.87290 ( 81) link_ALPHA1-6 : bond 0.00977 ( 24) link_ALPHA1-6 : angle 1.80344 ( 72) link_BETA1-4 : bond 0.00780 ( 69) link_BETA1-4 : angle 2.22802 ( 207) link_NAG-ASN : bond 0.00715 ( 64) link_NAG-ASN : angle 2.74264 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 265 time to evaluate : 0.698 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: O 115 TYR cc_start: 0.4844 (m-80) cc_final: 0.4459 (m-80) REVERT: M 3 GLN cc_start: 0.6029 (mp10) cc_final: 0.4424 (tm-30) REVERT: M 79 LEU cc_start: 0.2558 (OUTLIER) cc_final: 0.2327 (tp) REVERT: M 81 LEU cc_start: -0.0572 (OUTLIER) cc_final: -0.1075 (tm) REVERT: M 83 MET cc_start: 0.1124 (OUTLIER) cc_final: 0.0282 (tpt) REVERT: N 3 VAL cc_start: 0.6547 (OUTLIER) cc_final: 0.5743 (t) REVERT: N 4 MET cc_start: 0.6025 (mpp) cc_final: 0.5502 (tpp) REVERT: Q 70 ILE cc_start: 0.2768 (pt) cc_final: 0.1894 (mt) REVERT: R 42 GLN cc_start: 0.3100 (tt0) cc_final: 0.2769 (tp40) REVERT: A 100 MET cc_start: -0.0299 (mtp) cc_final: -0.0625 (tpt) REVERT: B 482 GLU cc_start: 0.4485 (mm-30) cc_final: 0.4081 (tp30) REVERT: C 258 GLN cc_start: 0.3036 (OUTLIER) cc_final: 0.2769 (tp-100) REVERT: D 537 LEU cc_start: 0.3102 (OUTLIER) cc_final: 0.2354 (tt) REVERT: D 650 GLN cc_start: -0.0902 (OUTLIER) cc_final: -0.1497 (tt0) REVERT: E 535 MET cc_start: 0.4325 (pmt) cc_final: 0.3421 (mmt) REVERT: E 550 GLN cc_start: 0.3246 (OUTLIER) cc_final: 0.2517 (mt0) REVERT: K 6 GLN cc_start: -0.0923 (tt0) cc_final: -0.1881 (pp30) REVERT: K 80 MET cc_start: 0.1226 (ptt) cc_final: 0.0806 (ttm) REVERT: I 100 TRP cc_start: 0.2222 (m-10) cc_final: -0.0918 (p90) REVERT: H 45 LYS cc_start: 0.3591 (OUTLIER) cc_final: 0.3204 (mppt) outliers start: 138 outliers final: 49 residues processed: 374 average time/residue: 0.4807 time to fit residues: 217.0751 Evaluate side-chains 277 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 62 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 282 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 258 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 82 GLN O 109 HIS ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 GLN ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 109 HIS R 32 ASN R 101 GLN A 33 ASN ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 352 HIS B 114 GLN B 130 GLN B 170 GLN B 203 GLN B 315 GLN ** B 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN E 590 GLN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN I 108 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.159540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.140609 restraints weight = 67996.270| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 3.59 r_work: 0.4117 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3500 moved from start: 0.9151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.216 27874 Z= 0.429 Angle : 1.524 30.822 38227 Z= 0.730 Chirality : 0.079 1.790 4749 Planarity : 0.010 0.120 4481 Dihedral : 13.540 146.164 7566 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 30.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.60 % Favored : 90.14 % Rotamer: Outliers : 8.86 % Allowed : 23.72 % Favored : 67.41 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.87 (0.13), residues: 3031 helix: -2.39 (0.23), residues: 363 sheet: -0.52 (0.18), residues: 816 loop : -2.59 (0.12), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG B 192 TYR 0.081 0.005 TYR C 217 PHE 0.048 0.006 PHE C 317 TRP 0.070 0.005 TRP F 623 HIS 0.082 0.005 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00921 (27617) covalent geometry : angle 1.46993 (37503) SS BOND : bond 0.01036 ( 47) SS BOND : angle 2.95361 ( 94) hydrogen bonds : bond 0.07552 ( 772) hydrogen bonds : angle 8.28349 ( 2007) link_ALPHA1-2 : bond 0.00824 ( 26) link_ALPHA1-2 : angle 2.47571 ( 78) link_ALPHA1-3 : bond 0.01398 ( 27) link_ALPHA1-3 : angle 2.26668 ( 81) link_ALPHA1-6 : bond 0.00930 ( 24) link_ALPHA1-6 : angle 2.43665 ( 72) link_BETA1-4 : bond 0.01837 ( 69) link_BETA1-4 : angle 3.24300 ( 207) link_NAG-ASN : bond 0.02422 ( 64) link_NAG-ASN : angle 4.26237 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 382 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 MET cc_start: 0.6717 (ttt) cc_final: 0.5007 (ttp) REVERT: O 51 MET cc_start: 0.7209 (mpp) cc_final: 0.5878 (ptm) REVERT: O 81 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5459 (pp) REVERT: P 13 VAL cc_start: 0.6431 (OUTLIER) cc_final: 0.6149 (p) REVERT: P 36 TYR cc_start: 0.3820 (OUTLIER) cc_final: 0.3334 (t80) REVERT: P 44 THR cc_start: 0.4270 (p) cc_final: 0.1452 (p) REVERT: M 3 GLN cc_start: 0.6035 (mp10) cc_final: 0.4633 (tm-30) REVERT: M 46 GLU cc_start: 0.3943 (OUTLIER) cc_final: 0.3737 (pm20) REVERT: M 51 MET cc_start: 0.1502 (mtm) cc_final: 0.0857 (tpp) REVERT: M 79 LEU cc_start: 0.2083 (OUTLIER) cc_final: 0.1364 (tp) REVERT: N 3 VAL cc_start: 0.6775 (OUTLIER) cc_final: 0.6405 (t) REVERT: A 69 TRP cc_start: 0.4386 (OUTLIER) cc_final: 0.2995 (m100) REVERT: A 85 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5858 (m-70) REVERT: A 100 MET cc_start: 0.0250 (mtp) cc_final: -0.0535 (tpt) REVERT: A 104 MET cc_start: 0.1891 (mtt) cc_final: 0.1511 (tpt) REVERT: A 159 PHE cc_start: 0.3088 (OUTLIER) cc_final: 0.2643 (p90) REVERT: A 175 LEU cc_start: 0.4713 (OUTLIER) cc_final: 0.3739 (tp) REVERT: A 178 ARG cc_start: 0.0556 (OUTLIER) cc_final: -0.2703 (pmt170) REVERT: A 216 HIS cc_start: 0.0292 (OUTLIER) cc_final: -0.0048 (m90) REVERT: A 305 LYS cc_start: 0.4974 (mtmt) cc_final: 0.4226 (ttpt) REVERT: A 427 TRP cc_start: 0.2353 (m-90) cc_final: 0.1334 (m100) REVERT: C 141 ASP cc_start: 0.3569 (OUTLIER) cc_final: 0.3216 (p0) REVERT: C 161 MET cc_start: 0.0784 (tpt) cc_final: 0.0468 (tpt) REVERT: C 166 ARG cc_start: 0.4967 (tmt170) cc_final: 0.3136 (ttt90) REVERT: C 272 ILE cc_start: 0.3929 (OUTLIER) cc_final: 0.3460 (mt) REVERT: C 286 VAL cc_start: 0.5127 (OUTLIER) cc_final: 0.4917 (m) REVERT: C 322 ILE cc_start: 0.1750 (OUTLIER) cc_final: 0.1382 (pp) REVERT: C 340 GLU cc_start: 0.6885 (tt0) cc_final: 0.6555 (mp0) REVERT: D 577 GLN cc_start: 0.4615 (OUTLIER) cc_final: 0.4199 (mm110) REVERT: D 591 GLN cc_start: 0.2590 (OUTLIER) cc_final: 0.1801 (mm110) REVERT: D 635 ILE cc_start: 0.2827 (OUTLIER) cc_final: 0.2539 (tp) REVERT: D 650 GLN cc_start: -0.0802 (OUTLIER) cc_final: -0.1176 (tt0) REVERT: E 550 GLN cc_start: 0.4283 (OUTLIER) cc_final: 0.3950 (pm20) REVERT: E 626 MET cc_start: 0.2698 (OUTLIER) cc_final: 0.2157 (tpp) REVERT: G 29 ILE cc_start: 0.5583 (OUTLIER) cc_final: 0.5235 (mt) REVERT: G 51 ILE cc_start: 0.5835 (OUTLIER) cc_final: 0.5600 (pt) REVERT: G 80 MET cc_start: 0.1341 (tmt) cc_final: 0.0012 (tmt) REVERT: I 71 TRP cc_start: 0.5147 (p90) cc_final: 0.4296 (p90) REVERT: L 35 TRP cc_start: 0.0502 (m-10) cc_final: -0.0997 (m100) REVERT: H 53 LYS cc_start: 0.6193 (mtmm) cc_final: 0.5970 (mtmm) REVERT: H 77 ASN cc_start: 0.7845 (t0) cc_final: 0.7636 (t0) REVERT: J 4 MET cc_start: 0.3420 (pmm) cc_final: 0.2506 (ptp) REVERT: J 39 ARG cc_start: 0.3185 (mmp-170) cc_final: 0.2635 (mmp80) REVERT: J 67 TRP cc_start: 0.6264 (t60) cc_final: 0.5926 (t60) outliers start: 238 outliers final: 73 residues processed: 563 average time/residue: 0.5102 time to fit residues: 343.3772 Evaluate side-chains 390 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 293 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 32 PHE Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 216 HIS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 397 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 546 SER Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 630 GLN Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 84 SER Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 78 optimal weight: 0.0670 chunk 189 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 243 optimal weight: 0.8980 chunk 196 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 117 GLN ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 HIS M 117 GLN Q 1 GLN ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 422 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN E 575 GLN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN I 59 ASN H 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.156991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.136520 restraints weight = 66987.598| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 3.60 r_work: 0.4054 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3455 moved from start: 0.9423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27874 Z= 0.181 Angle : 0.993 18.794 38227 Z= 0.454 Chirality : 0.055 0.781 4749 Planarity : 0.006 0.084 4481 Dihedral : 11.096 92.903 7566 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.62 % Allowed : 30.09 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.14), residues: 3031 helix: -1.33 (0.25), residues: 372 sheet: -0.16 (0.17), residues: 912 loop : -2.29 (0.13), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 500 TYR 0.027 0.002 TYR Q 50 PHE 0.031 0.002 PHE P 99 TRP 0.025 0.002 TRP C 96 HIS 0.010 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00387 (27617) covalent geometry : angle 0.92896 (37503) SS BOND : bond 0.00557 ( 47) SS BOND : angle 2.06343 ( 94) hydrogen bonds : bond 0.04470 ( 772) hydrogen bonds : angle 6.49059 ( 2007) link_ALPHA1-2 : bond 0.00612 ( 26) link_ALPHA1-2 : angle 1.90178 ( 78) link_ALPHA1-3 : bond 0.01174 ( 27) link_ALPHA1-3 : angle 2.14485 ( 81) link_ALPHA1-6 : bond 0.01073 ( 24) link_ALPHA1-6 : angle 1.85905 ( 72) link_BETA1-4 : bond 0.00665 ( 69) link_BETA1-4 : angle 2.18218 ( 207) link_NAG-ASN : bond 0.00895 ( 64) link_NAG-ASN : angle 3.96879 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 313 time to evaluate : 0.867 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: O 2 MET cc_start: 0.6909 (ttt) cc_final: 0.6582 (tpt) REVERT: O 19 ARG cc_start: 0.7404 (ptm160) cc_final: 0.7162 (ptm160) REVERT: O 60 TYR cc_start: 0.5550 (OUTLIER) cc_final: 0.5041 (m-80) REVERT: O 81 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.4718 (tp) REVERT: O 83 MET cc_start: 0.5283 (ptm) cc_final: 0.5067 (ptm) REVERT: M 18 LEU cc_start: -0.0264 (OUTLIER) cc_final: -0.1286 (pt) REVERT: M 51 MET cc_start: 0.1472 (mtm) cc_final: 0.0940 (tpp) REVERT: R 104 LYS cc_start: 0.5448 (tptp) cc_final: 0.4981 (mmmt) REVERT: A 100 MET cc_start: 0.0392 (mtp) cc_final: -0.0266 (tpt) REVERT: A 104 MET cc_start: 0.1905 (mtt) cc_final: 0.1075 (tpt) REVERT: A 434 MET cc_start: 0.2995 (ppp) cc_final: 0.2514 (tpt) REVERT: A 475 MET cc_start: 0.3392 (mpp) cc_final: 0.3141 (mtp) REVERT: B 100 MET cc_start: 0.2982 (pp-130) cc_final: 0.1284 (mmt) REVERT: C 161 MET cc_start: 0.1586 (tpt) cc_final: 0.1150 (tpt) REVERT: C 166 ARG cc_start: 0.5120 (tmt170) cc_final: 0.3483 (ttt90) REVERT: C 322 ILE cc_start: 0.1931 (OUTLIER) cc_final: 0.1501 (pp) REVERT: C 492 GLU cc_start: 0.3569 (OUTLIER) cc_final: 0.0657 (tp30) REVERT: D 537 LEU cc_start: 0.3879 (OUTLIER) cc_final: 0.3019 (tt) REVERT: D 591 GLN cc_start: 0.2898 (OUTLIER) cc_final: 0.2416 (mm110) REVERT: D 626 MET cc_start: 0.5743 (ptt) cc_final: 0.4701 (ppp) REVERT: E 535 MET cc_start: 0.4654 (pmt) cc_final: 0.3643 (mmt) REVERT: E 550 GLN cc_start: 0.3597 (OUTLIER) cc_final: 0.2692 (mt0) REVERT: E 626 MET cc_start: 0.2318 (mmm) cc_final: 0.2074 (tpp) REVERT: G 17 SER cc_start: 0.1823 (m) cc_final: 0.1422 (p) REVERT: G 29 ILE cc_start: 0.5804 (OUTLIER) cc_final: 0.5409 (mt) REVERT: I 71 TRP cc_start: 0.5065 (p90) cc_final: 0.4343 (p90) REVERT: L 4 MET cc_start: 0.4068 (mmm) cc_final: 0.3500 (mmm) REVERT: H 53 LYS cc_start: 0.6483 (mtmm) cc_final: 0.6222 (mtmm) REVERT: H 77 ASN cc_start: 0.7655 (t0) cc_final: 0.7413 (t0) REVERT: J 4 MET cc_start: 0.3347 (pmm) cc_final: 0.2581 (ptp) REVERT: J 39 ARG cc_start: 0.3239 (mmt180) cc_final: 0.2741 (mmp80) outliers start: 124 outliers final: 48 residues processed: 402 average time/residue: 0.4795 time to fit residues: 232.6625 Evaluate side-chains 314 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 257 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 25 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 263 optimal weight: 0.5980 chunk 267 optimal weight: 0.0470 chunk 38 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 35 HIS ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN Q 80 HIS R 101 GLN A 82 GLN ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN F 540 GLN F 616 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 59 ASN H 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.157667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.137247 restraints weight = 67674.800| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.70 r_work: 0.4059 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3633 moved from start: 0.9864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 27874 Z= 0.163 Angle : 0.922 18.878 38227 Z= 0.422 Chirality : 0.052 0.563 4749 Planarity : 0.005 0.075 4481 Dihedral : 9.982 93.922 7566 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.43 % Allowed : 30.47 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -1.91 (0.14), residues: 3031 helix: -0.89 (0.26), residues: 369 sheet: 0.08 (0.17), residues: 888 loop : -2.18 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG P 18 TYR 0.020 0.002 TYR K 27 PHE 0.030 0.002 PHE B 223 TRP 0.047 0.002 TRP A 395 HIS 0.006 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00359 (27617) covalent geometry : angle 0.86228 (37503) SS BOND : bond 0.00478 ( 47) SS BOND : angle 1.80679 ( 94) hydrogen bonds : bond 0.03936 ( 772) hydrogen bonds : angle 6.08156 ( 2007) link_ALPHA1-2 : bond 0.00627 ( 26) link_ALPHA1-2 : angle 1.83490 ( 78) link_ALPHA1-3 : bond 0.01220 ( 27) link_ALPHA1-3 : angle 2.18423 ( 81) link_ALPHA1-6 : bond 0.00913 ( 24) link_ALPHA1-6 : angle 1.89383 ( 72) link_BETA1-4 : bond 0.00610 ( 69) link_BETA1-4 : angle 2.02486 ( 207) link_NAG-ASN : bond 0.00736 ( 64) link_NAG-ASN : angle 3.66618 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 275 time to evaluate : 0.936 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: O 2 MET cc_start: 0.6939 (ttt) cc_final: 0.5914 (ttp) REVERT: O 46 GLU cc_start: 0.7232 (pp20) cc_final: 0.6943 (pm20) REVERT: O 60 TYR cc_start: 0.5631 (OUTLIER) cc_final: 0.5376 (m-80) REVERT: O 81 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.4742 (tp) REVERT: M 6 GLU cc_start: 0.6195 (mp0) cc_final: 0.3229 (pm20) REVERT: M 20 LEU cc_start: 0.3850 (OUTLIER) cc_final: 0.3258 (mp) REVERT: M 51 MET cc_start: 0.1732 (mtm) cc_final: 0.1122 (tpp) REVERT: M 79 LEU cc_start: -0.0252 (OUTLIER) cc_final: -0.0529 (tm) REVERT: Q 27 PHE cc_start: 0.4305 (m-10) cc_final: 0.4092 (m-80) REVERT: A 100 MET cc_start: 0.0450 (mtp) cc_final: -0.0322 (tpt) REVERT: A 104 MET cc_start: 0.1855 (mtt) cc_final: 0.1041 (tpt) REVERT: A 276 ASN cc_start: -0.1448 (OUTLIER) cc_final: -0.2741 (p0) REVERT: B 100 MET cc_start: 0.3291 (pp-130) cc_final: 0.0933 (mmt) REVERT: B 126 CYS cc_start: 0.4683 (OUTLIER) cc_final: 0.4236 (p) REVERT: B 323 ILE cc_start: 0.8110 (tt) cc_final: 0.7706 (pp) REVERT: C 166 ARG cc_start: 0.5195 (tmt170) cc_final: 0.3212 (ttt90) REVERT: C 322 ILE cc_start: 0.1903 (OUTLIER) cc_final: 0.1489 (pp) REVERT: C 492 GLU cc_start: 0.3530 (OUTLIER) cc_final: 0.0777 (tp30) REVERT: D 537 LEU cc_start: 0.3643 (OUTLIER) cc_final: 0.2921 (tt) REVERT: D 591 GLN cc_start: 0.3393 (OUTLIER) cc_final: 0.2805 (mm110) REVERT: D 626 MET cc_start: 0.5612 (ptt) cc_final: 0.4989 (ppp) REVERT: F 530 MET cc_start: 0.1425 (mpm) cc_final: 0.0008 (ppp) REVERT: F 601 LYS cc_start: 0.1090 (OUTLIER) cc_final: 0.0848 (ttpt) REVERT: K 23 GLU cc_start: 0.1839 (OUTLIER) cc_final: 0.1534 (tp30) REVERT: K 80 MET cc_start: 0.5256 (tpt) cc_final: 0.4602 (ttp) REVERT: G 29 ILE cc_start: 0.6001 (OUTLIER) cc_final: 0.5588 (mt) REVERT: G 64 GLN cc_start: 0.4354 (mm-40) cc_final: 0.3910 (mm-40) REVERT: G 109 VAL cc_start: 0.6974 (t) cc_final: 0.6568 (m) REVERT: I 71 TRP cc_start: 0.5105 (p90) cc_final: 0.4303 (p90) REVERT: I 80 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.3572 (mmm) REVERT: L 4 MET cc_start: 0.4133 (mmm) cc_final: 0.3471 (mmm) REVERT: H 53 LYS cc_start: 0.6593 (mtmm) cc_final: 0.6260 (mtmm) REVERT: J 4 MET cc_start: 0.3382 (pmm) cc_final: 0.2743 (ptp) REVERT: J 89 GLN cc_start: 0.2887 (tp40) cc_final: 0.0985 (mt0) outliers start: 119 outliers final: 61 residues processed: 368 average time/residue: 0.4567 time to fit residues: 206.1181 Evaluate side-chains 327 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 252 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain F residue 586 TYR Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 160 optimal weight: 0.0040 chunk 185 optimal weight: 0.6980 chunk 289 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 167 optimal weight: 0.0370 chunk 231 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 overall best weight: 0.5072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 HIS R 90 HIS R 101 GLN A 105 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.158192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.137904 restraints weight = 67584.920| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 3.68 r_work: 0.4069 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3744 moved from start: 1.0241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27874 Z= 0.150 Angle : 0.879 14.249 38227 Z= 0.403 Chirality : 0.050 0.556 4749 Planarity : 0.005 0.073 4481 Dihedral : 9.171 93.617 7563 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.10 % Allowed : 31.43 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -1.72 (0.14), residues: 3031 helix: -0.59 (0.26), residues: 369 sheet: 0.09 (0.17), residues: 900 loop : -2.03 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 19 TYR 0.022 0.002 TYR K 27 PHE 0.021 0.002 PHE K 63 TRP 0.030 0.002 TRP J 67 HIS 0.013 0.001 HIS N 90 Details of bonding type rmsd covalent geometry : bond 0.00328 (27617) covalent geometry : angle 0.82650 (37503) SS BOND : bond 0.00671 ( 47) SS BOND : angle 1.77171 ( 94) hydrogen bonds : bond 0.03715 ( 772) hydrogen bonds : angle 5.83893 ( 2007) link_ALPHA1-2 : bond 0.00661 ( 26) link_ALPHA1-2 : angle 1.74576 ( 78) link_ALPHA1-3 : bond 0.01116 ( 27) link_ALPHA1-3 : angle 2.06879 ( 81) link_ALPHA1-6 : bond 0.00942 ( 24) link_ALPHA1-6 : angle 1.76119 ( 72) link_BETA1-4 : bond 0.00547 ( 69) link_BETA1-4 : angle 1.83191 ( 207) link_NAG-ASN : bond 0.00663 ( 64) link_NAG-ASN : angle 3.29646 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 278 time to evaluate : 1.152 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: O 2 MET cc_start: 0.7082 (ttt) cc_final: 0.6299 (ttp) REVERT: O 51 MET cc_start: 0.6793 (mpp) cc_final: 0.6391 (mtp) REVERT: O 60 TYR cc_start: 0.5684 (OUTLIER) cc_final: 0.5389 (m-80) REVERT: O 81 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.4952 (tp) REVERT: M 6 GLU cc_start: 0.5968 (mp0) cc_final: 0.1336 (tp30) REVERT: M 51 MET cc_start: 0.1599 (mtm) cc_final: 0.0997 (tpp) REVERT: M 79 LEU cc_start: -0.1027 (OUTLIER) cc_final: -0.1292 (tm) REVERT: N 4 MET cc_start: 0.5509 (tpp) cc_final: 0.5058 (tmm) REVERT: Q 27 PHE cc_start: 0.4349 (m-10) cc_final: 0.3848 (m-80) REVERT: Q 28 ASP cc_start: 0.2662 (OUTLIER) cc_final: 0.2277 (t0) REVERT: A 100 MET cc_start: 0.0489 (mtp) cc_final: -0.0223 (tpt) REVERT: A 104 MET cc_start: 0.1625 (mtt) cc_final: 0.0771 (tpt) REVERT: A 276 ASN cc_start: -0.1571 (OUTLIER) cc_final: -0.2758 (p0) REVERT: A 434 MET cc_start: 0.2860 (pp-130) cc_final: 0.2298 (tpt) REVERT: B 104 MET cc_start: 0.6017 (tmm) cc_final: 0.5249 (tmt) REVERT: B 126 CYS cc_start: 0.5230 (OUTLIER) cc_final: 0.4520 (p) REVERT: B 276 ASN cc_start: 0.4991 (OUTLIER) cc_final: 0.3537 (t0) REVERT: B 323 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7866 (pp) REVERT: C 104 MET cc_start: 0.2931 (mmt) cc_final: 0.2533 (tpp) REVERT: C 166 ARG cc_start: 0.5566 (tmt170) cc_final: 0.3314 (ttt180) REVERT: C 322 ILE cc_start: 0.2111 (OUTLIER) cc_final: 0.1669 (pp) REVERT: C 426 MET cc_start: 0.3226 (ptm) cc_final: 0.2775 (mtm) REVERT: D 537 LEU cc_start: 0.3895 (OUTLIER) cc_final: 0.3271 (tt) REVERT: D 591 GLN cc_start: 0.3343 (OUTLIER) cc_final: 0.2932 (mm110) REVERT: D 626 MET cc_start: 0.5424 (ptt) cc_final: 0.4874 (ppp) REVERT: E 550 GLN cc_start: 0.4865 (OUTLIER) cc_final: 0.4636 (tp-100) REVERT: K 23 GLU cc_start: 0.1842 (OUTLIER) cc_final: 0.1543 (tp30) REVERT: K 80 MET cc_start: 0.5495 (tpt) cc_final: 0.4693 (ttt) REVERT: G 64 GLN cc_start: 0.4514 (mm-40) cc_final: 0.4219 (mm-40) REVERT: G 80 MET cc_start: 0.3360 (ppp) cc_final: 0.2987 (ppp) REVERT: L 4 MET cc_start: 0.4158 (mmm) cc_final: 0.3542 (mmm) REVERT: L 35 TRP cc_start: 0.0918 (m-10) cc_final: 0.0153 (m100) REVERT: L 36 TYR cc_start: 0.2529 (m-10) cc_final: 0.0773 (m-10) REVERT: J 4 MET cc_start: 0.3421 (pmm) cc_final: 0.2813 (ptp) REVERT: J 89 GLN cc_start: 0.3169 (tp40) cc_final: 0.1208 (mt0) outliers start: 110 outliers final: 60 residues processed: 358 average time/residue: 0.4642 time to fit residues: 203.2085 Evaluate side-chains 322 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 249 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 419 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 135 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 259 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 0.0670 chunk 266 optimal weight: 0.8980 chunk 192 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 96 optimal weight: 0.0970 chunk 243 optimal weight: 0.0020 overall best weight: 0.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 74 ASN Q 80 HIS R 101 GLN ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN J 38 GLN J 69 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.159281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.138930 restraints weight = 67710.860| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 3.75 r_work: 0.4079 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3843 moved from start: 1.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27874 Z= 0.141 Angle : 0.845 14.155 38227 Z= 0.387 Chirality : 0.049 0.496 4749 Planarity : 0.005 0.070 4481 Dihedral : 8.368 91.689 7563 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.65 % Allowed : 32.14 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -1.53 (0.15), residues: 3031 helix: -0.30 (0.27), residues: 369 sheet: 0.26 (0.17), residues: 867 loop : -1.93 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 39 TYR 0.023 0.002 TYR K 27 PHE 0.034 0.002 PHE K 63 TRP 0.034 0.002 TRP A 338 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00310 (27617) covalent geometry : angle 0.79952 (37503) SS BOND : bond 0.00445 ( 47) SS BOND : angle 1.53042 ( 94) hydrogen bonds : bond 0.03431 ( 772) hydrogen bonds : angle 5.61014 ( 2007) link_ALPHA1-2 : bond 0.00699 ( 26) link_ALPHA1-2 : angle 1.68724 ( 78) link_ALPHA1-3 : bond 0.01111 ( 27) link_ALPHA1-3 : angle 2.03897 ( 81) link_ALPHA1-6 : bond 0.00977 ( 24) link_ALPHA1-6 : angle 1.74591 ( 72) link_BETA1-4 : bond 0.00532 ( 69) link_BETA1-4 : angle 1.72695 ( 207) link_NAG-ASN : bond 0.00566 ( 64) link_NAG-ASN : angle 3.00275 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 293 time to evaluate : 0.944 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: O 2 MET cc_start: 0.7154 (ttt) cc_final: 0.6361 (ttp) REVERT: O 35 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6839 (t70) REVERT: O 46 GLU cc_start: 0.7208 (pp20) cc_final: 0.6974 (pm20) REVERT: O 51 MET cc_start: 0.6711 (mpp) cc_final: 0.6403 (mtp) REVERT: O 81 LEU cc_start: 0.5411 (OUTLIER) cc_final: 0.5107 (tp) REVERT: P 42 GLN cc_start: 0.7409 (mt0) cc_final: 0.6851 (mp-120) REVERT: M 6 GLU cc_start: 0.5838 (mp0) cc_final: 0.1232 (tp30) REVERT: M 51 MET cc_start: 0.1506 (mtm) cc_final: 0.0850 (tpp) REVERT: M 79 LEU cc_start: -0.1395 (OUTLIER) cc_final: -0.1607 (tm) REVERT: N 58 VAL cc_start: 0.3971 (p) cc_final: 0.3754 (m) REVERT: Q 27 PHE cc_start: 0.4545 (m-10) cc_final: 0.3797 (m-80) REVERT: Q 28 ASP cc_start: 0.2788 (OUTLIER) cc_final: 0.2366 (t0) REVERT: R 87 TYR cc_start: 0.0984 (OUTLIER) cc_final: 0.0528 (t80) REVERT: R 101 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7284 (pp30) REVERT: A 100 MET cc_start: 0.0671 (mtp) cc_final: 0.0112 (mmt) REVERT: A 104 MET cc_start: 0.1733 (mtt) cc_final: 0.1329 (tpt) REVERT: A 135 THR cc_start: -0.0764 (OUTLIER) cc_final: -0.1044 (m) REVERT: A 276 ASN cc_start: -0.1624 (OUTLIER) cc_final: -0.2605 (p0) REVERT: B 100 MET cc_start: 0.3606 (pp-130) cc_final: 0.0805 (mmt) REVERT: B 101 VAL cc_start: 0.1907 (OUTLIER) cc_final: 0.1604 (p) REVERT: B 276 ASN cc_start: 0.5173 (OUTLIER) cc_final: 0.3708 (t0) REVERT: B 323 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8017 (pp) REVERT: C 104 MET cc_start: 0.3046 (mmt) cc_final: 0.2806 (tpp) REVERT: C 150 MET cc_start: 0.3481 (mtm) cc_final: 0.3057 (mpp) REVERT: C 166 ARG cc_start: 0.5416 (tmt170) cc_final: 0.2720 (ttt90) REVERT: C 322 ILE cc_start: 0.2014 (OUTLIER) cc_final: 0.1646 (pp) REVERT: C 492 GLU cc_start: 0.3268 (OUTLIER) cc_final: 0.0849 (tp30) REVERT: D 535 MET cc_start: 0.6149 (tmt) cc_final: 0.5932 (ttt) REVERT: D 537 LEU cc_start: 0.3635 (OUTLIER) cc_final: 0.3303 (tt) REVERT: D 626 MET cc_start: 0.5338 (ptt) cc_final: 0.4699 (ppp) REVERT: K 23 GLU cc_start: 0.1905 (OUTLIER) cc_final: 0.1662 (tp30) REVERT: K 80 MET cc_start: 0.5556 (tpt) cc_final: 0.4956 (ttt) REVERT: K 82 LEU cc_start: 0.6813 (mm) cc_final: 0.6025 (tt) REVERT: G 80 MET cc_start: 0.3688 (ppp) cc_final: 0.3356 (ppp) REVERT: I 80 MET cc_start: 0.4472 (OUTLIER) cc_final: 0.4125 (mmm) REVERT: L 4 MET cc_start: 0.4660 (mmm) cc_final: 0.2242 (mpt) REVERT: L 36 TYR cc_start: 0.2577 (m-10) cc_final: 0.0809 (m-10) REVERT: J 4 MET cc_start: 0.3313 (pmm) cc_final: 0.2805 (ptp) REVERT: J 89 GLN cc_start: 0.3117 (tp40) cc_final: 0.1366 (mt0) outliers start: 98 outliers final: 57 residues processed: 362 average time/residue: 0.4615 time to fit residues: 203.5873 Evaluate side-chains 332 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 259 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 90 HIS Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 87 TYR Chi-restraints excluded: chain R residue 101 GLN Chi-restraints excluded: chain A residue 105 HIS Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 80 MET Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 190 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 266 optimal weight: 0.1980 chunk 181 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 HIS ** R 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 HIS ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS B 280 ASN B 478 ASN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS C 462 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.165564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.145553 restraints weight = 71519.989| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 4.13 r_work: 0.4149 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5295 moved from start: 1.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.206 27874 Z= 0.296 Angle : 1.161 17.242 38227 Z= 0.561 Chirality : 0.061 0.494 4749 Planarity : 0.009 0.262 4481 Dihedral : 8.980 92.540 7563 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.07 % Favored : 90.86 % Rotamer: Outliers : 4.58 % Allowed : 31.55 % Favored : 63.87 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.14), residues: 3031 helix: -1.64 (0.24), residues: 369 sheet: -0.41 (0.17), residues: 914 loop : -2.18 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG F 617 TYR 0.049 0.004 TYR A 177 PHE 0.098 0.004 PHE A 361 TRP 0.051 0.004 TRP Q 122 HIS 0.019 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00655 (27617) covalent geometry : angle 1.11077 (37503) SS BOND : bond 0.01001 ( 47) SS BOND : angle 2.43076 ( 94) hydrogen bonds : bond 0.05422 ( 772) hydrogen bonds : angle 7.03867 ( 2007) link_ALPHA1-2 : bond 0.00877 ( 26) link_ALPHA1-2 : angle 2.19402 ( 78) link_ALPHA1-3 : bond 0.01020 ( 27) link_ALPHA1-3 : angle 2.07782 ( 81) link_ALPHA1-6 : bond 0.00978 ( 24) link_ALPHA1-6 : angle 1.89935 ( 72) link_BETA1-4 : bond 0.00718 ( 69) link_BETA1-4 : angle 2.32446 ( 207) link_NAG-ASN : bond 0.01074 ( 64) link_NAG-ASN : angle 3.67898 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 401 time to evaluate : 0.798 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: O 21 SER cc_start: 0.6499 (m) cc_final: 0.6177 (p) REVERT: O 32 PHE cc_start: 0.5093 (m-80) cc_final: 0.4741 (t80) REVERT: O 51 MET cc_start: 0.6921 (mpp) cc_final: 0.6313 (ttm) REVERT: O 65 LYS cc_start: 0.7577 (mmtt) cc_final: 0.7370 (mmtt) REVERT: O 84 ASP cc_start: 0.7854 (m-30) cc_final: 0.7254 (p0) REVERT: O 101 ILE cc_start: 0.8650 (pt) cc_final: 0.8339 (pt) REVERT: O 119 MET cc_start: 0.4684 (ptm) cc_final: 0.4323 (ptp) REVERT: P 17 GLU cc_start: 0.7376 (pp20) cc_final: 0.7166 (pp20) REVERT: P 24 ARG cc_start: 0.7095 (pmm-80) cc_final: 0.6676 (pmm150) REVERT: P 36 TYR cc_start: 0.4150 (OUTLIER) cc_final: 0.3257 (t80) REVERT: P 42 GLN cc_start: 0.7385 (mt0) cc_final: 0.6846 (mp-120) REVERT: P 46 VAL cc_start: 0.8696 (t) cc_final: 0.8407 (m) REVERT: P 104 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7514 (tppt) REVERT: M 34 MET cc_start: 0.1645 (ttt) cc_final: 0.1157 (pmt) REVERT: M 51 MET cc_start: 0.2149 (mtm) cc_final: 0.1342 (mmm) REVERT: M 83 MET cc_start: 0.1346 (mmt) cc_final: 0.0378 (tmm) REVERT: N 4 MET cc_start: 0.6557 (mmm) cc_final: 0.6277 (tpt) REVERT: Q 28 ASP cc_start: 0.4314 (OUTLIER) cc_final: 0.3842 (t0) REVERT: R 104 LYS cc_start: 0.5852 (tptp) cc_final: 0.5249 (mmmt) REVERT: A 100 MET cc_start: 0.1094 (mtp) cc_final: 0.0057 (tpt) REVERT: A 135 THR cc_start: 0.2020 (OUTLIER) cc_final: 0.1776 (m) REVERT: A 276 ASN cc_start: -0.1521 (OUTLIER) cc_final: -0.2504 (p0) REVERT: A 287 GLN cc_start: 0.2548 (mm-40) cc_final: 0.1687 (mm-40) REVERT: A 434 MET cc_start: 0.3429 (OUTLIER) cc_final: 0.2576 (mmm) REVERT: A 475 MET cc_start: 0.4648 (mpp) cc_final: 0.3823 (mtt) REVERT: B 74 CYS cc_start: -0.0512 (OUTLIER) cc_final: -0.0979 (m) REVERT: B 100 MET cc_start: 0.5191 (pp-130) cc_final: 0.4883 (ppp) REVERT: B 104 MET cc_start: 0.6901 (tmm) cc_final: 0.6297 (tmt) REVERT: B 284 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8173 (mt) REVERT: B 466 GLU cc_start: 0.6348 (mt-10) cc_final: 0.6017 (mm-30) REVERT: C 141 ASP cc_start: 0.6600 (t70) cc_final: 0.5921 (p0) REVERT: C 150 MET cc_start: 0.4639 (mtm) cc_final: 0.3145 (mpp) REVERT: C 151 ARG cc_start: 0.7567 (ttp80) cc_final: 0.7325 (ttm110) REVERT: C 166 ARG cc_start: 0.5865 (tmt170) cc_final: 0.2821 (tmt-80) REVERT: C 373 THR cc_start: 0.7846 (m) cc_final: 0.7156 (p) REVERT: C 462 ASN cc_start: 0.5122 (OUTLIER) cc_final: 0.4836 (m-40) REVERT: D 591 GLN cc_start: 0.3060 (OUTLIER) cc_final: 0.2555 (mm110) REVERT: D 626 MET cc_start: 0.5607 (ptt) cc_final: 0.4520 (ppp) REVERT: D 635 ILE cc_start: 0.4550 (OUTLIER) cc_final: 0.4306 (tp) REVERT: E 550 GLN cc_start: 0.5239 (OUTLIER) cc_final: 0.4979 (tp-100) REVERT: E 626 MET cc_start: 0.2633 (mmm) cc_final: 0.2404 (tpp) REVERT: K 71 ARG cc_start: 0.4261 (OUTLIER) cc_final: 0.3135 (ptt90) REVERT: K 82 LYS cc_start: 0.7078 (mmpt) cc_final: 0.6719 (mmtp) REVERT: G 76 TYR cc_start: 0.7550 (m-80) cc_final: 0.7340 (m-80) REVERT: G 98 ASP cc_start: 0.8574 (m-30) cc_final: 0.8129 (t0) REVERT: I 92 CYS cc_start: 0.1498 (OUTLIER) cc_final: 0.1235 (p) REVERT: L 4 MET cc_start: 0.4619 (mmm) cc_final: 0.3901 (mmm) REVERT: L 35 TRP cc_start: 0.1523 (m-10) cc_final: 0.0556 (m100) REVERT: H 53 LYS cc_start: 0.6728 (mtmt) cc_final: 0.6404 (mppt) REVERT: J 4 MET cc_start: 0.3896 (pmm) cc_final: 0.3478 (ptp) outliers start: 123 outliers final: 54 residues processed: 486 average time/residue: 0.4813 time to fit residues: 282.5293 Evaluate side-chains 375 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 308 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 654 GLU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 62 PHE Chi-restraints excluded: chain J residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 249 optimal weight: 8.9990 chunk 276 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 121 optimal weight: 0.0970 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 109 HIS Q 80 HIS ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 377 ASN C 98 ASN C 422 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN J 79 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.165695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.144556 restraints weight = 71291.735| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 4.04 r_work: 0.4146 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 moved from start: 1.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 27874 Z= 0.180 Angle : 1.007 21.287 38227 Z= 0.469 Chirality : 0.053 0.533 4749 Planarity : 0.005 0.082 4481 Dihedral : 8.414 92.147 7563 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 2.57 % Allowed : 35.83 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -2.04 (0.14), residues: 3031 helix: -1.31 (0.24), residues: 393 sheet: -0.26 (0.17), residues: 927 loop : -2.06 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 61 TYR 0.042 0.002 TYR C 191 PHE 0.028 0.002 PHE K 63 TRP 0.043 0.003 TRP A 96 HIS 0.012 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00403 (27617) covalent geometry : angle 0.94233 (37503) SS BOND : bond 0.00501 ( 47) SS BOND : angle 2.56209 ( 94) hydrogen bonds : bond 0.04102 ( 772) hydrogen bonds : angle 6.42645 ( 2007) link_ALPHA1-2 : bond 0.00584 ( 26) link_ALPHA1-2 : angle 1.80763 ( 78) link_ALPHA1-3 : bond 0.00997 ( 27) link_ALPHA1-3 : angle 1.97369 ( 81) link_ALPHA1-6 : bond 0.00922 ( 24) link_ALPHA1-6 : angle 1.75113 ( 72) link_BETA1-4 : bond 0.00571 ( 69) link_BETA1-4 : angle 1.92855 ( 207) link_NAG-ASN : bond 0.00786 ( 64) link_NAG-ASN : angle 4.14453 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6062 Ramachandran restraints generated. 3031 Oldfield, 0 Emsley, 3031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 364 time to evaluate : 0.810 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: O 2 MET cc_start: 0.7554 (ttm) cc_final: 0.7306 (ttp) REVERT: O 3 GLN cc_start: 0.6880 (tp-100) cc_final: 0.6545 (tt0) REVERT: O 21 SER cc_start: 0.6494 (m) cc_final: 0.6064 (p) REVERT: O 32 PHE cc_start: 0.5289 (m-80) cc_final: 0.4431 (t80) REVERT: O 35 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7590 (t-170) REVERT: O 51 MET cc_start: 0.6750 (mpp) cc_final: 0.6442 (ttm) REVERT: O 65 LYS cc_start: 0.7394 (mmtt) cc_final: 0.7166 (mmtt) REVERT: O 81 LEU cc_start: 0.6260 (OUTLIER) cc_final: 0.5776 (tm) REVERT: O 84 ASP cc_start: 0.7951 (m-30) cc_final: 0.7192 (p0) REVERT: O 99 ASP cc_start: 0.7382 (m-30) cc_final: 0.6253 (m-30) REVERT: O 101 ILE cc_start: 0.8667 (pt) cc_final: 0.8342 (pt) REVERT: O 119 MET cc_start: 0.4408 (OUTLIER) cc_final: 0.4020 (ptt) REVERT: P 36 TYR cc_start: 0.3828 (OUTLIER) cc_final: 0.3392 (t80) REVERT: P 42 GLN cc_start: 0.7309 (mt0) cc_final: 0.6733 (mp-120) REVERT: P 46 VAL cc_start: 0.8736 (t) cc_final: 0.8351 (m) REVERT: P 104 LYS cc_start: 0.8208 (ttpp) cc_final: 0.7586 (tppt) REVERT: M 34 MET cc_start: 0.1274 (ttt) cc_final: 0.0929 (pmt) REVERT: M 45 LEU cc_start: 0.3026 (tp) cc_final: 0.2516 (mt) REVERT: M 51 MET cc_start: 0.2209 (mtm) cc_final: 0.1436 (mmm) REVERT: Q 27 PHE cc_start: 0.4658 (m-80) cc_final: 0.4450 (m-80) REVERT: Q 28 ASP cc_start: 0.4648 (OUTLIER) cc_final: 0.4121 (t0) REVERT: A 100 MET cc_start: 0.1432 (mtp) cc_final: 0.0729 (mmt) REVERT: A 104 MET cc_start: 0.2570 (mtt) cc_final: 0.1397 (tpt) REVERT: A 135 THR cc_start: 0.2404 (OUTLIER) cc_final: 0.2023 (m) REVERT: A 276 ASN cc_start: -0.1291 (OUTLIER) cc_final: -0.2145 (p0) REVERT: A 287 GLN cc_start: 0.2216 (mm-40) cc_final: 0.1671 (mm-40) REVERT: A 434 MET cc_start: 0.3460 (pp-130) cc_final: 0.2389 (tpt) REVERT: A 475 MET cc_start: 0.4234 (mpp) cc_final: 0.3693 (mtt) REVERT: B 104 MET cc_start: 0.6939 (tmm) cc_final: 0.6183 (tmt) REVERT: B 166 ARG cc_start: 0.2961 (tpt170) cc_final: 0.1864 (tmt170) REVERT: B 178 ARG cc_start: 0.7833 (ptp-170) cc_final: 0.7341 (ptm-80) REVERT: B 273 ARG cc_start: 0.6797 (mmt90) cc_final: 0.6572 (mtp85) REVERT: B 284 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8125 (mt) REVERT: B 323 ILE cc_start: 0.8580 (pp) cc_final: 0.8370 (pp) REVERT: C 86 LEU cc_start: 0.3019 (mt) cc_final: 0.2585 (mp) REVERT: C 141 ASP cc_start: 0.6811 (t70) cc_final: 0.6160 (p0) REVERT: C 150 MET cc_start: 0.4472 (mtm) cc_final: 0.3547 (mpp) REVERT: C 166 ARG cc_start: 0.5962 (tmt170) cc_final: 0.2884 (tmt-80) REVERT: C 287 GLN cc_start: 0.5981 (tt0) cc_final: 0.5751 (tt0) REVERT: C 373 THR cc_start: 0.8065 (m) cc_final: 0.7463 (p) REVERT: D 537 LEU cc_start: 0.4332 (OUTLIER) cc_final: 0.4000 (tm) REVERT: D 626 MET cc_start: 0.5705 (ptt) cc_final: 0.4783 (ppp) REVERT: D 634 GLU cc_start: 0.6950 (tt0) cc_final: 0.6649 (pt0) REVERT: E 610 TRP cc_start: 0.2643 (m-10) cc_final: 0.2230 (t-100) REVERT: K 82 LYS cc_start: 0.7264 (mmpt) cc_final: 0.6973 (mmtp) REVERT: G 98 ASP cc_start: 0.8403 (m-30) cc_final: 0.7933 (t0) REVERT: G 107 THR cc_start: 0.6528 (m) cc_final: 0.5707 (m) REVERT: I 53 LYS cc_start: 0.7840 (ttmt) cc_final: 0.6689 (mmtt) REVERT: I 61 ARG cc_start: 0.6079 (tpm170) cc_final: 0.5310 (tpm170) REVERT: L 4 MET cc_start: 0.4534 (mmm) cc_final: 0.2282 (mpt) REVERT: J 73 LEU cc_start: 0.3960 (tm) cc_final: 0.3039 (mt) outliers start: 69 outliers final: 36 residues processed: 416 average time/residue: 0.4995 time to fit residues: 249.4158 Evaluate side-chains 347 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 119 MET Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain M residue 106 SER Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 28 ASP Chi-restraints excluded: chain Q residue 94 TYR Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 14 SER Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 179 optimal weight: 0.0770 chunk 72 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 104 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 270 optimal weight: 7.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 HIS ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN C 98 ASN C 377 ASN C 422 GLN C 428 GLN C 462 ASN F 616 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.165362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.144030 restraints weight = 70093.571| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 4.16 r_work: 0.4126 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 1.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 27874 Z= 0.169 Angle : 1.000 22.152 38227 Z= 0.464 Chirality : 0.054 0.780 4749 Planarity : 0.006 0.137 4481 Dihedral : 7.976 89.702 7563 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.64 % Allowed : 36.09 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.14), residues: 3031 helix: -0.97 (0.25), residues: 393 sheet: -0.18 (0.17), residues: 914 loop : -2.00 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 588 TYR 0.165 0.002 TYR Q 94 PHE 0.029 0.002 PHE K 63 TRP 0.036 0.002 TRP J 67 HIS 0.010 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00381 (27617) covalent geometry : angle 0.93691 (37503) SS BOND : bond 0.00456 ( 47) SS BOND : angle 2.32177 ( 94) hydrogen bonds : bond 0.04021 ( 772) hydrogen bonds : angle 6.25176 ( 2007) link_ALPHA1-2 : bond 0.00685 ( 26) link_ALPHA1-2 : angle 1.77538 ( 78) link_ALPHA1-3 : bond 0.00985 ( 27) link_ALPHA1-3 : angle 1.92896 ( 81) link_ALPHA1-6 : bond 0.00863 ( 24) link_ALPHA1-6 : angle 1.66934 ( 72) link_BETA1-4 : bond 0.00552 ( 69) link_BETA1-4 : angle 1.86625 ( 207) link_NAG-ASN : bond 0.00785 ( 64) link_NAG-ASN : angle 4.18613 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9633.88 seconds wall clock time: 164 minutes 44.04 seconds (9884.04 seconds total)