Starting phenix.real_space_refine on Sun Jul 5 09:35:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pc2_13316/07_2026/7pc2_13316.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pc2_13316/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7pc2_13316/07_2026/7pc2_13316.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pc2_13316/07_2026/7pc2_13316.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pc2_13316/07_2026/7pc2_13316.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pc2_13316/07_2026/7pc2_13316.map" model { file = "/net/cci-nas-00/data/ceres_data/7pc2_13316/07_2026/7pc2_13316.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pc2_13316/07_2026/7pc2_13316.cif" } 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-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 6.23, per 1000 atoms: 0.23 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: 3.67 Conformation dependent library (CDL) restraints added in 1.2 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: 0.79 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: 5.99 Time building geometry restraints manager: 4.56 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 - 17.95: 13116 17.95 - 35.90: 1315 35.90 - 53.85: 319 53.85 - 71.80: 86 71.80 - 89.75: 22 Dihedral angle restraints: 14858 sinusoidal: 5970 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 14855 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 27.300 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0524 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 : 15.682 89.753 9017 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/Z covalent geometry : bond 0.03313 / 2.31 (27617) covalent geometry : angle 1.65859 / 1.14 (37503) SS BOND : bond 0.20221 / 11.45 ( 47) SS BOND : angle 10.39840 / 5.18 ( 94) hydrogen bonds : bond 0.24173 / 15.67 ( 772) hydrogen bonds : angle 8.14022 / 5.51 ( 2007) link_ALPHA1-2 : bond 0.00220 / 0.12 ( 26) link_ALPHA1-2 : angle 2.20964 / 1.44 ( 78) link_ALPHA1-3 : bond 0.00347 / 0.22 ( 27) link_ALPHA1-3 : angle 2.29227 / 1.43 ( 81) link_ALPHA1-6 : bond 0.00419 / 0.25 ( 24) link_ALPHA1-6 : angle 1.94271 / 1.26 ( 72) link_BETA1-4 : bond 0.00529 / 0.34 ( 69) link_BETA1-4 : angle 2.50715 / 1.73 ( 207) link_NAG-ASN : bond 0.01074 / 0.82 ( 64) link_NAG-ASN : angle 3.03442 / 1.65 ( 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 : 0.905 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: 0.5931 time to fit residues: 367.6206 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 : 0.930 ------------------------------------------------------------------------------- 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... ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN O 74 ASN 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 33 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 ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.126295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.096729 restraints weight = 58433.697| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 3.38 r_work: 0.3413 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1050 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27874 Z= 0.169 Angle : 0.870 13.632 38227 Z= 0.417 Chirality : 0.050 0.589 4749 Planarity : 0.005 0.077 4481 Dihedral : 6.007 76.152 3369 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 5.18 % Allowed : 22.12 % Favored : 72.70 % 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: -2.73 (0.14), residues: 3031 helix: -2.38 (0.21), residues: 405 sheet: -0.78 (0.16), residues: 1026 loop : -2.40 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 72 TYR 0.028 0.002 TYR L 32 PHE 0.036 0.002 PHE A 159 TRP 0.037 0.002 TRP N 94 HIS 0.018 0.002 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (27617) covalent geometry : angle 0.82191 / 0.41 (37503) SS BOND : bond 0.00594 / 0.34 ( 47) SS BOND : angle 1.91781 / 1.19 ( 94) hydrogen bonds : bond 0.05026 / 3.36 ( 772) hydrogen bonds : angle 5.95714 / 4.08 ( 2007) link_ALPHA1-2 : bond 0.00457 / 0.29 ( 26) link_ALPHA1-2 : angle 2.10169 / 1.41 ( 78) link_ALPHA1-3 : bond 0.00672 / 0.42 ( 27) link_ALPHA1-3 : angle 1.71907 / 1.08 ( 81) link_ALPHA1-6 : bond 0.00568 / 0.35 ( 24) link_ALPHA1-6 : angle 1.50158 / 0.94 ( 72) link_BETA1-4 : bond 0.00725 / 0.48 ( 69) link_BETA1-4 : angle 2.10032 / 1.45 ( 207) link_NAG-ASN : bond 0.00990 / 0.66 ( 64) link_NAG-ASN : angle 2.91083 / 1.78 ( 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 442 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 303 time to evaluate : 0.954 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: P 99 PHE cc_start: 0.3242 (OUTLIER) cc_final: 0.3031 (m-10) REVERT: M 20 LEU cc_start: 0.5268 (OUTLIER) cc_final: 0.4994 (tt) REVERT: M 79 LEU cc_start: 0.2835 (tp) cc_final: 0.2485 (tp) REVERT: M 81 LEU cc_start: -0.0908 (OUTLIER) cc_final: -0.1131 (tm) REVERT: M 83 MET cc_start: 0.1751 (OUTLIER) cc_final: 0.1189 (tpt) REVERT: N 4 MET cc_start: 0.5701 (mpp) cc_final: 0.4511 (tpp) REVERT: N 108 LYS cc_start: -0.5217 (OUTLIER) cc_final: -0.5456 (tttm) REVERT: Q 34 MET cc_start: 0.1364 (OUTLIER) cc_final: 0.0595 (mpt) REVERT: Q 83 MET cc_start: 0.4354 (pmm) cc_final: 0.2386 (tpt) REVERT: R 42 GLN cc_start: 0.3157 (tt0) cc_final: 0.2745 (tp40) REVERT: A 100 MET cc_start: -0.0200 (mtp) cc_final: -0.0675 (tpt) REVERT: A 166 ARG cc_start: -0.2820 (OUTLIER) cc_final: -0.4499 (tpt90) REVERT: A 205 CYS cc_start: -0.1549 (OUTLIER) cc_final: -0.2348 (t) REVERT: A 298 ARG cc_start: 0.3305 (tmm-80) cc_final: 0.3048 (ttt180) REVERT: A 341 THR cc_start: 0.0335 (p) cc_final: -0.2008 (m) REVERT: A 426 MET cc_start: 0.0191 (pmm) cc_final: -0.1750 (mpt) REVERT: B 96 TRP cc_start: 0.4683 (m-90) cc_final: 0.3886 (m100) REVERT: C 258 GLN cc_start: 0.3096 (OUTLIER) cc_final: 0.2716 (tp40) REVERT: C 335 LYS cc_start: 0.1511 (OUTLIER) cc_final: 0.1164 (tptt) REVERT: D 537 LEU cc_start: 0.3233 (OUTLIER) cc_final: 0.2348 (tt) REVERT: E 550 GLN cc_start: 0.3106 (OUTLIER) cc_final: 0.2524 (mt0) REVERT: K 6 GLN cc_start: -0.1535 (tt0) cc_final: -0.2270 (pm20) REVERT: K 80 MET cc_start: 0.1068 (ptt) cc_final: 0.0543 (ttm) REVERT: G 51 ILE cc_start: 0.0459 (tt) cc_final: -0.0249 (mm) REVERT: G 82 LEU cc_start: 0.0926 (tp) cc_final: 0.0585 (mm) REVERT: I 100 TRP cc_start: 0.2097 (m100) cc_final: -0.1323 (p90) REVERT: L 42 LYS cc_start: 0.3655 (mmtm) cc_final: 0.3111 (pptt) REVERT: H 45 LYS cc_start: 0.3807 (OUTLIER) cc_final: 0.3402 (ptpp) REVERT: J 21 ILE cc_start: 0.1942 (OUTLIER) cc_final: 0.1610 (tt) outliers start: 139 outliers final: 31 residues processed: 408 average time/residue: 0.5032 time to fit residues: 247.2051 Evaluate side-chains 262 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 166 ARG Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 276 ASN 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 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 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 21 ILE 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: 6.9990 chunk 93 optimal weight: 5.9990 chunk 205 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 164 optimal weight: 0.0870 chunk 34 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 109 HIS Q 109 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN B 356 ASN C 258 GLN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN ** E 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS G 59 ASN G 62 GLN I 59 ASN J 79 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.134713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107390 restraints weight = 60698.681| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.45 r_work: 0.3613 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1750 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 27874 Z= 0.205 Angle : 0.904 13.419 38227 Z= 0.430 Chirality : 0.051 0.536 4749 Planarity : 0.006 0.081 4481 Dihedral : 5.775 81.834 3360 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.17 % Favored : 93.80 % Rotamer: Outliers : 5.81 % Allowed : 23.76 % Favored : 70.43 % Cbeta Deviations : 0.04 % 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: -2.07 (0.14), residues: 3031 helix: -1.41 (0.24), residues: 384 sheet: -0.20 (0.16), residues: 960 loop : -2.16 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 500 TYR 0.022 0.002 TYR H 36 PHE 0.031 0.003 PHE A 159 TRP 0.028 0.003 TRP Q 36 HIS 0.014 0.002 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (27617) covalent geometry : angle 0.85737 / 0.42 (37503) SS BOND : bond 0.01279 / 0.88 ( 47) SS BOND : angle 1.72117 / 1.09 ( 94) hydrogen bonds : bond 0.04680 / 3.15 ( 772) hydrogen bonds : angle 5.86008 / 4.02 ( 2007) link_ALPHA1-2 : bond 0.00553 / 0.34 ( 26) link_ALPHA1-2 : angle 1.87911 / 1.23 ( 78) link_ALPHA1-3 : bond 0.00678 / 0.43 ( 27) link_ALPHA1-3 : angle 1.68888 / 1.08 ( 81) link_ALPHA1-6 : bond 0.00536 / 0.34 ( 24) link_ALPHA1-6 : angle 1.59408 / 1.01 ( 72) link_BETA1-4 : bond 0.01026 / 0.75 ( 69) link_BETA1-4 : angle 2.09025 / 1.38 ( 207) link_NAG-ASN : bond 0.01592 / 0.79 ( 64) link_NAG-ASN : angle 3.05396 / 1.88 ( 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 450 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 294 time to evaluate : 1.011 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 19 ARG cc_start: 0.4193 (ptm-80) cc_final: 0.3873 (ptm-80) REVERT: O 115 TYR cc_start: 0.5432 (m-80) cc_final: 0.5148 (m-80) REVERT: M 3 GLN cc_start: 0.5890 (mp10) cc_final: 0.4355 (tm-30) REVERT: M 20 LEU cc_start: 0.5069 (OUTLIER) cc_final: 0.4840 (tt) REVERT: M 79 LEU cc_start: 0.2495 (OUTLIER) cc_final: 0.2251 (tp) REVERT: M 81 LEU cc_start: -0.0392 (OUTLIER) cc_final: -0.0989 (tm) REVERT: M 83 MET cc_start: 0.0945 (OUTLIER) cc_final: 0.0355 (tpt) REVERT: N 3 VAL cc_start: 0.6631 (OUTLIER) cc_final: 0.5813 (t) REVERT: N 4 MET cc_start: 0.6098 (mpp) cc_final: 0.5343 (tpp) REVERT: R 42 GLN cc_start: 0.3289 (tt0) cc_final: 0.2914 (tp40) REVERT: R 101 GLN cc_start: 0.7099 (pp30) cc_final: 0.6834 (pp30) REVERT: A 100 MET cc_start: -0.0146 (mtp) cc_final: -0.0579 (tpt) REVERT: A 104 MET cc_start: 0.1250 (mtt) cc_final: 0.0853 (tpt) REVERT: A 247 CYS cc_start: 0.2633 (OUTLIER) cc_final: 0.2289 (p) REVERT: A 298 ARG cc_start: 0.4128 (tmm-80) cc_final: 0.3661 (ttt-90) REVERT: C 258 GLN cc_start: 0.3259 (OUTLIER) cc_final: 0.2167 (tp-100) REVERT: C 338 TRP cc_start: 0.4862 (t-100) cc_final: 0.3495 (t60) REVERT: D 537 LEU cc_start: 0.3385 (OUTLIER) cc_final: 0.2176 (tt) REVERT: E 535 MET cc_start: 0.4342 (pmt) cc_final: 0.3491 (mmt) REVERT: E 550 GLN cc_start: 0.3359 (OUTLIER) cc_final: 0.2635 (mt0) REVERT: I 100 TRP cc_start: 0.2340 (m-10) cc_final: 0.1619 (m100) REVERT: L 42 LYS cc_start: 0.3938 (mmtm) cc_final: 0.3420 (pptt) REVERT: H 45 LYS cc_start: 0.3983 (OUTLIER) cc_final: 0.3671 (mppt) outliers start: 156 outliers final: 55 residues processed: 414 average time/residue: 0.4567 time to fit residues: 229.8883 Evaluate side-chains 309 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 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 105 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 20 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 14 SER Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 43 SER 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 178 ARG Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS 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 161 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 106 THR 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 373 THR 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 D residue 647 GLU Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain I residue 47 TRP 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 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 52 SER Chi-restraints excluded: chain J residue 78 LEU 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: 9.9990 chunk 54 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 274 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 264 optimal weight: 1.9990 chunk 258 optimal weight: 0.7980 chunk 151 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 GLN ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 GLN ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 GLN R 101 GLN A 105 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 203 GLN B 315 GLN C 195 ASN C 258 GLN C 352 HIS D 607 ASN D 650 GLN E 540 GLN E 575 GLN E 591 GLN E 651 ASN K 59 ASN I 108 GLN H 37 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.144264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.119863 restraints weight = 62181.426| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.45 r_work: 0.3800 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2458 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 27874 Z= 0.203 Angle : 0.951 26.009 38227 Z= 0.447 Chirality : 0.053 0.915 4749 Planarity : 0.007 0.250 4481 Dihedral : 5.878 81.844 3360 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.40 % Favored : 93.57 % Rotamer: Outliers : 5.96 % Allowed : 24.92 % Favored : 69.12 % Cbeta Deviations : 0.04 % 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: -1.78 (0.14), residues: 3031 helix: -1.10 (0.24), residues: 402 sheet: 0.03 (0.17), residues: 915 loop : -1.97 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 67 TYR 0.033 0.002 TYR L 36 PHE 0.022 0.002 PHE I 33 TRP 0.043 0.003 TRP F 623 HIS 0.009 0.002 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (27617) covalent geometry : angle 0.90858 / 0.44 (37503) SS BOND : bond 0.01928 / 1.11 ( 47) SS BOND : angle 1.81660 / 1.16 ( 94) hydrogen bonds : bond 0.04334 / 2.92 ( 772) hydrogen bonds : angle 5.95968 / 4.07 ( 2007) link_ALPHA1-2 : bond 0.00448 / 0.29 ( 26) link_ALPHA1-2 : angle 1.79569 / 1.19 ( 78) link_ALPHA1-3 : bond 0.00657 / 0.42 ( 27) link_ALPHA1-3 : angle 1.67510 / 1.05 ( 81) link_ALPHA1-6 : bond 0.00559 / 0.36 ( 24) link_ALPHA1-6 : angle 1.57367 / 0.97 ( 72) link_BETA1-4 : bond 0.00570 / 0.38 ( 69) link_BETA1-4 : angle 1.99736 / 1.32 ( 207) link_NAG-ASN : bond 0.00745 / 0.44 ( 64) link_NAG-ASN : angle 3.10924 / 1.93 ( 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 473 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 313 time to evaluate : 0.884 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: O 6 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6116 (pm20) REVERT: O 22 CYS cc_start: 0.4563 (m) cc_final: 0.4053 (t) REVERT: M 1 GLN cc_start: 0.3308 (OUTLIER) cc_final: 0.2984 (tm-30) REVERT: M 2 MET cc_start: 0.4878 (OUTLIER) cc_final: 0.4423 (pmm) REVERT: M 3 GLN cc_start: 0.5871 (mp10) cc_final: 0.4394 (tm-30) REVERT: M 20 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5016 (tt) REVERT: M 51 MET cc_start: 0.1028 (mtm) cc_final: 0.0378 (tpp) REVERT: M 83 MET cc_start: 0.0588 (OUTLIER) cc_final: 0.0271 (mtt) REVERT: N 3 VAL cc_start: 0.6729 (OUTLIER) cc_final: 0.6206 (t) REVERT: N 21 LEU cc_start: 0.5740 (mp) cc_final: 0.5246 (tt) REVERT: Q 70 ILE cc_start: 0.3733 (OUTLIER) cc_final: 0.2995 (tp) REVERT: Q 80 HIS cc_start: 0.2509 (OUTLIER) cc_final: 0.2072 (m-70) REVERT: Q 87 ARG cc_start: 0.6521 (mpt-90) cc_final: 0.6154 (mtt90) REVERT: R 42 GLN cc_start: 0.3552 (tt0) cc_final: 0.3112 (tp40) REVERT: A 100 MET cc_start: 0.0033 (mtp) cc_final: -0.0809 (tpt) REVERT: A 104 MET cc_start: 0.2162 (mtt) cc_final: 0.1336 (tpt) REVERT: A 161 MET cc_start: 0.3225 (mpt) cc_final: 0.2345 (tpp) REVERT: A 247 CYS cc_start: 0.3066 (OUTLIER) cc_final: 0.2201 (p) REVERT: A 305 LYS cc_start: 0.3161 (mtmt) cc_final: 0.2729 (ttpt) REVERT: B 100 MET cc_start: 0.2367 (pp-130) cc_final: 0.0934 (mmt) REVERT: B 384 TYR cc_start: 0.3772 (m-80) cc_final: 0.2701 (m-10) REVERT: C 166 ARG cc_start: 0.4178 (tmt170) cc_final: 0.3063 (ttt90) REVERT: C 322 ILE cc_start: 0.0722 (OUTLIER) cc_final: 0.0142 (mt) REVERT: C 338 TRP cc_start: 0.5590 (t-100) cc_final: 0.5037 (t-100) REVERT: C 426 MET cc_start: 0.3237 (OUTLIER) cc_final: 0.2710 (mtm) REVERT: D 647 GLU cc_start: 0.4877 (OUTLIER) cc_final: 0.4438 (pt0) REVERT: E 550 GLN cc_start: 0.4017 (OUTLIER) cc_final: 0.2552 (mt0) REVERT: I 71 TRP cc_start: 0.4856 (p90) cc_final: 0.4108 (p90) REVERT: I 100 TRP cc_start: 0.2821 (m-10) cc_final: 0.2410 (m100) REVERT: L 35 TRP cc_start: -0.0359 (m-10) cc_final: -0.1125 (m100) REVERT: H 45 LYS cc_start: 0.4469 (OUTLIER) cc_final: 0.4227 (mppt) outliers start: 160 outliers final: 68 residues processed: 432 average time/residue: 0.4823 time to fit residues: 252.5637 Evaluate side-chains 337 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 255 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 12 VAL 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 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 104 LYS Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 2 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 80 HIS Chi-restraints excluded: chain Q residue 95 TYR Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 THR 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 101 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 322 ILE 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 570 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 591 GLN Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 550 GLN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 107 THR 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 7 SER 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 98 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 78 optimal weight: 0.0980 chunk 189 optimal weight: 0.5980 chunk 293 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 243 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 295 optimal weight: 9.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 GLN C 195 ASN C 352 HIS D 607 ASN E 575 GLN ** E 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.146087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.121811 restraints weight = 62135.294| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 3.53 r_work: 0.3831 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2485 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27874 Z= 0.135 Angle : 0.822 14.309 38227 Z= 0.378 Chirality : 0.046 0.442 4749 Planarity : 0.004 0.069 4481 Dihedral : 5.426 83.483 3360 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.47 % Allowed : 27.78 % Favored : 67.75 % 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: -1.52 (0.14), residues: 3031 helix: -0.54 (0.26), residues: 402 sheet: 0.22 (0.17), residues: 924 loop : -1.91 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 30 TYR 0.022 0.002 TYR C 217 PHE 0.021 0.001 PHE A 159 TRP 0.044 0.002 TRP C 427 HIS 0.016 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (27617) covalent geometry : angle 0.76804 / 0.37 (37503) SS BOND : bond 0.00479 / 0.28 ( 47) SS BOND : angle 1.77339 / 1.14 ( 94) hydrogen bonds : bond 0.03616 / 2.39 ( 772) hydrogen bonds : angle 5.54885 / 3.78 ( 2007) link_ALPHA1-2 : bond 0.00449 / 0.28 ( 26) link_ALPHA1-2 : angle 1.73469 / 1.13 ( 78) link_ALPHA1-3 : bond 0.00646 / 0.41 ( 27) link_ALPHA1-3 : angle 1.62880 / 1.03 ( 81) link_ALPHA1-6 : bond 0.00500 / 0.31 ( 24) link_ALPHA1-6 : angle 1.46983 / 0.92 ( 72) link_BETA1-4 : bond 0.00564 / 0.37 ( 69) link_BETA1-4 : angle 1.68574 / 1.15 ( 207) link_NAG-ASN : bond 0.00557 / 0.31 ( 64) link_NAG-ASN : angle 3.41832 / 2.01 ( 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 392 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 272 time to evaluate : 0.928 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 6 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.6185 (pm20) REVERT: O 7 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.7173 (p) REVERT: O 22 CYS cc_start: 0.4547 (m) cc_final: 0.3934 (t) REVERT: O 34 MET cc_start: 0.6254 (tpp) cc_final: 0.5704 (tpp) REVERT: O 51 MET cc_start: 0.6670 (mpp) cc_final: 0.5386 (ptm) REVERT: M 3 GLN cc_start: 0.5834 (mp10) cc_final: 0.4294 (tm-30) REVERT: M 6 GLU cc_start: 0.6364 (mp0) cc_final: 0.1671 (tp30) REVERT: M 51 MET cc_start: 0.0863 (mtm) cc_final: 0.0371 (tpp) REVERT: N 21 LEU cc_start: 0.5739 (mp) cc_final: 0.5206 (tt) REVERT: Q 90 ASP cc_start: 0.3345 (OUTLIER) cc_final: 0.3142 (t0) REVERT: R 42 GLN cc_start: 0.3420 (tt0) cc_final: 0.3024 (tp40) REVERT: R 105 LEU cc_start: 0.5873 (mm) cc_final: 0.5111 (pp) REVERT: A 100 MET cc_start: 0.0378 (mtp) cc_final: -0.0381 (tpt) REVERT: A 104 MET cc_start: 0.1908 (mtt) cc_final: 0.1284 (tpt) REVERT: A 161 MET cc_start: 0.3173 (mpt) cc_final: 0.2703 (tpp) REVERT: A 178 ARG cc_start: -0.1177 (OUTLIER) cc_final: -0.1382 (tpp80) REVERT: A 247 CYS cc_start: 0.2963 (OUTLIER) cc_final: 0.2124 (p) REVERT: A 298 ARG cc_start: 0.4723 (tmm-80) cc_final: 0.4052 (ttt90) REVERT: B 100 MET cc_start: 0.2400 (OUTLIER) cc_final: 0.0258 (mmt) REVERT: B 284 ILE cc_start: 0.1731 (mt) cc_final: 0.1404 (mt) REVERT: B 293 GLN cc_start: 0.4024 (pp30) cc_final: 0.3655 (tt0) REVERT: B 318 TYR cc_start: 0.7183 (m-80) cc_final: 0.5484 (m-80) REVERT: B 384 TYR cc_start: 0.3989 (m-80) cc_final: 0.2810 (m-10) REVERT: B 475 MET cc_start: 0.4656 (mmp) cc_final: 0.4171 (mmt) REVERT: C 150 MET cc_start: 0.2858 (OUTLIER) cc_final: 0.2570 (mtp) REVERT: C 166 ARG cc_start: 0.4022 (tmt170) cc_final: 0.2923 (ttt90) REVERT: C 338 TRP cc_start: 0.5502 (t-100) cc_final: 0.4972 (t-100) REVERT: C 426 MET cc_start: 0.3361 (ptt) cc_final: 0.2820 (ptp) REVERT: E 535 MET cc_start: 0.4599 (pmt) cc_final: 0.3569 (mmt) REVERT: E 550 GLN cc_start: 0.3806 (OUTLIER) cc_final: 0.2571 (mt0) REVERT: I 71 TRP cc_start: 0.4798 (p90) cc_final: 0.4088 (p90) REVERT: I 100 TRP cc_start: 0.2891 (m-10) cc_final: 0.2553 (m100) REVERT: L 4 MET cc_start: 0.3865 (mmm) cc_final: 0.3252 (mmm) REVERT: J 4 MET cc_start: 0.2879 (pmm) cc_final: 0.1721 (ptp) REVERT: J 39 ARG cc_start: 0.2710 (mmt180) cc_final: 0.2377 (mmp80) outliers start: 120 outliers final: 73 residues processed: 356 average time/residue: 0.4753 time to fit residues: 206.0666 Evaluate side-chains 328 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 247 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 12 VAL 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 96 CYS Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 36 TYR Chi-restraints excluded: chain P residue 104 LYS Chi-restraints excluded: chain P residue 105 LEU Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 90 ASP Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 178 ARG Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 255 VAL 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 100 MET Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 277 ILE Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR 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 E residue 595 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 83 ILE 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 Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 20 THR Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 78 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: 2.9990 chunk 139 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 263 optimal weight: 0.6980 chunk 267 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 117 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 32 ASN ** R 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 101 GLN A 82 GLN A 170 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 280 ASN ** B 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 GLN E 575 GLN E 590 GLN K 64 GLN G 59 ASN G 95 GLN I 39 GLN I 59 ASN H 37 GLN J 38 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.161774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.142840 restraints weight = 69338.817| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 3.70 r_work: 0.4136 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3923 moved from start: 1.0222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 27874 Z= 0.295 Angle : 1.202 24.938 38227 Z= 0.567 Chirality : 0.062 0.814 4749 Planarity : 0.008 0.095 4481 Dihedral : 6.806 87.179 3360 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.55 % Favored : 91.42 % Rotamer: Outliers : 7.23 % Allowed : 26.48 % Favored : 66.29 % 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: -2.20 (0.14), residues: 3031 helix: -1.32 (0.26), residues: 359 sheet: -0.47 (0.16), residues: 1019 loop : -2.21 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG A 429 TYR 0.052 0.004 TYR C 384 PHE 0.052 0.004 PHE A 159 TRP 0.064 0.005 TRP A 112 HIS 0.016 0.003 HIS Q 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.29 (27617) covalent geometry : angle 1.14817 / 0.56 (37503) SS BOND : bond 0.00811 / 0.51 ( 47) SS BOND : angle 2.19317 / 1.36 ( 94) hydrogen bonds : bond 0.05705 / 3.82 ( 772) hydrogen bonds : angle 6.97502 / 4.80 ( 2007) link_ALPHA1-2 : bond 0.00557 / 0.37 ( 26) link_ALPHA1-2 : angle 1.87766 / 1.22 ( 78) link_ALPHA1-3 : bond 0.00684 / 0.42 ( 27) link_ALPHA1-3 : angle 1.65609 / 1.02 ( 81) link_ALPHA1-6 : bond 0.00570 / 0.37 ( 24) link_ALPHA1-6 : angle 1.63633 / 1.03 ( 72) link_BETA1-4 : bond 0.01174 / 0.86 ( 69) link_BETA1-4 : angle 2.43675 / 1.74 ( 207) link_NAG-ASN : bond 0.01227 / 0.86 ( 64) link_NAG-ASN : angle 4.20434 / 3.03 ( 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 547 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 353 time to evaluate : 0.827 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: O 2 MET cc_start: 0.6439 (ttt) cc_final: 0.5269 (ttp) REVERT: O 6 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6299 (pm20) REVERT: O 34 MET cc_start: 0.6700 (tpp) cc_final: 0.6329 (tpp) REVERT: O 51 MET cc_start: 0.7327 (mpp) cc_final: 0.6356 (mtp) REVERT: O 64 VAL cc_start: 0.5115 (m) cc_final: 0.4841 (m) REVERT: O 81 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.4525 (tm) REVERT: O 111 TYR cc_start: 0.6388 (t80) cc_final: 0.6046 (t80) REVERT: P 42 GLN cc_start: 0.7489 (mt0) cc_final: 0.7280 (mt0) REVERT: P 104 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6933 (tppt) REVERT: M 51 MET cc_start: 0.1955 (mtm) cc_final: 0.1584 (mtp) REVERT: Q 83 MET cc_start: 0.4822 (pmm) cc_final: 0.4208 (pmm) REVERT: A 69 TRP cc_start: 0.4353 (OUTLIER) cc_final: 0.3259 (m100) REVERT: A 85 HIS cc_start: 0.6540 (OUTLIER) cc_final: 0.6029 (m-70) REVERT: A 100 MET cc_start: 0.0312 (mtp) cc_final: -0.0448 (tpt) REVERT: A 104 MET cc_start: 0.1836 (mtt) cc_final: 0.1177 (tpt) REVERT: A 161 MET cc_start: 0.3147 (mpt) cc_final: 0.2870 (tpp) REVERT: A 247 CYS cc_start: 0.2952 (OUTLIER) cc_final: 0.2348 (p) REVERT: A 276 ASN cc_start: -0.1595 (OUTLIER) cc_final: -0.2863 (p0) REVERT: A 326 ILE cc_start: 0.3905 (OUTLIER) cc_final: 0.3689 (mm) REVERT: A 420 ILE cc_start: 0.5820 (OUTLIER) cc_final: 0.5483 (tt) REVERT: A 434 MET cc_start: 0.4366 (ppp) cc_final: 0.3750 (ppp) REVERT: A 475 MET cc_start: 0.2950 (OUTLIER) cc_final: 0.2728 (mtm) REVERT: B 474 ASP cc_start: 0.6305 (p0) cc_final: 0.5982 (p0) REVERT: B 475 MET cc_start: 0.7212 (mmp) cc_final: 0.6938 (mmt) REVERT: C 166 ARG cc_start: 0.5548 (tmt170) cc_final: 0.2280 (tmt-80) REVERT: D 591 GLN cc_start: 0.3065 (OUTLIER) cc_final: 0.2362 (mm110) REVERT: D 626 MET cc_start: 0.4700 (tmt) cc_final: 0.4302 (ptm) REVERT: D 635 ILE cc_start: 0.3442 (OUTLIER) cc_final: 0.3214 (tp) REVERT: F 530 MET cc_start: 0.1921 (pp-130) cc_final: 0.1484 (mpp) REVERT: F 658 GLN cc_start: 0.4865 (OUTLIER) cc_final: 0.4643 (pm20) REVERT: K 80 MET cc_start: 0.5557 (tpt) cc_final: 0.4992 (ttp) REVERT: K 82 LYS cc_start: 0.3477 (OUTLIER) cc_final: 0.3154 (mmpt) REVERT: G 23 GLU cc_start: 0.3234 (OUTLIER) cc_final: 0.3008 (mp0) REVERT: G 51 ILE cc_start: 0.6964 (OUTLIER) cc_final: 0.6291 (tt) REVERT: L 4 MET cc_start: 0.4596 (mmm) cc_final: 0.4025 (mmm) REVERT: H 71 TYR cc_start: 0.4828 (m-80) cc_final: 0.4472 (m-80) REVERT: H 77 ASN cc_start: 0.7997 (t0) cc_final: 0.7457 (t0) REVERT: J 4 MET cc_start: 0.3409 (pmm) cc_final: 0.2614 (ptp) REVERT: J 89 GLN cc_start: 0.3107 (tp40) cc_final: 0.1328 (mt0) outliers start: 194 outliers final: 72 residues processed: 504 average time/residue: 0.4527 time to fit residues: 277.3410 Evaluate side-chains 365 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 277 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 6 GLU Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 81 LEU Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain P residue 3 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 P residue 73 LEU Chi-restraints excluded: chain P residue 104 LYS Chi-restraints excluded: chain M residue 83 MET 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 53 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 68 PHE Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain Q residue 105 CYS Chi-restraints excluded: chain Q residue 127 THR Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 THR 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 A residue 467 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 123 THR 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 286 VAL Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 373 THR 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 658 GLN Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain G residue 23 GLU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 74 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 H residue 87 PHE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 14 SER 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 62 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 160 optimal weight: 6.9990 chunk 185 optimal weight: 0.6980 chunk 289 optimal weight: 0.5980 chunk 224 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 chunk 231 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 268 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 228 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN M 117 GLN N 92 ASN Q 1 GLN R 6 GLN R 90 HIS R 101 GLN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 280 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN C 422 GLN E 575 GLN F 540 GLN G 3 GLN ** G 71AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.161077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.141610 restraints weight = 68073.053| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 3.66 r_work: 0.4123 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3998 moved from start: 1.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27874 Z= 0.157 Angle : 0.916 14.361 38227 Z= 0.424 Chirality : 0.049 0.432 4749 Planarity : 0.005 0.069 4481 Dihedral : 5.772 41.958 3357 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.95 % Allowed : 31.36 % Favored : 64.69 % 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: -1.77 (0.14), residues: 3031 helix: -0.73 (0.26), residues: 383 sheet: 0.01 (0.17), residues: 951 loop : -2.07 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 304 TYR 0.027 0.002 TYR D 643 PHE 0.035 0.002 PHE K 63 TRP 0.028 0.002 TRP J 67 HIS 0.010 0.001 HIS G 71A Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (27617) covalent geometry : angle 0.86612 / 0.41 (37503) SS BOND : bond 0.00577 / 0.38 ( 47) SS BOND : angle 1.78431 / 1.14 ( 94) hydrogen bonds : bond 0.03917 / 2.61 ( 772) hydrogen bonds : angle 6.15106 / 4.23 ( 2007) link_ALPHA1-2 : bond 0.00441 / 0.26 ( 26) link_ALPHA1-2 : angle 1.63285 / 1.08 ( 78) link_ALPHA1-3 : bond 0.00639 / 0.41 ( 27) link_ALPHA1-3 : angle 1.67883 / 1.06 ( 81) link_ALPHA1-6 : bond 0.00531 / 0.33 ( 24) link_ALPHA1-6 : angle 1.46200 / 0.91 ( 72) link_BETA1-4 : bond 0.00591 / 0.39 ( 69) link_BETA1-4 : angle 1.91098 / 1.35 ( 207) link_NAG-ASN : bond 0.00706 / 0.41 ( 64) link_NAG-ASN : angle 3.46521 / 2.26 ( 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 408 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 302 time to evaluate : 0.824 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: O 2 MET cc_start: 0.6252 (ttt) cc_final: 0.5418 (ttm) REVERT: O 34 MET cc_start: 0.6685 (tpp) cc_final: 0.6363 (tpp) REVERT: O 51 MET cc_start: 0.6943 (mpp) cc_final: 0.6430 (mtp) REVERT: O 64 VAL cc_start: 0.5329 (m) cc_final: 0.5081 (m) REVERT: O 81 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.4730 (tp) REVERT: P 2 ILE cc_start: 0.7179 (mm) cc_final: 0.6709 (mt) REVERT: P 104 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.6996 (tppt) REVERT: P 106 GLU cc_start: 0.6895 (pm20) cc_final: 0.6652 (pm20) REVERT: M 1 GLN cc_start: 0.2551 (OUTLIER) cc_final: 0.2254 (tm-30) REVERT: M 51 MET cc_start: 0.1606 (mtm) cc_final: 0.0991 (tpp) REVERT: R 87 TYR cc_start: 0.0981 (OUTLIER) cc_final: 0.0473 (t80) REVERT: R 101 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7460 (pp30) REVERT: A 100 MET cc_start: 0.0526 (mtp) cc_final: -0.0230 (tpt) REVERT: A 104 MET cc_start: 0.1974 (mtt) cc_final: 0.1356 (tpt) REVERT: A 247 CYS cc_start: 0.2931 (OUTLIER) cc_final: 0.2109 (p) REVERT: A 276 ASN cc_start: -0.1627 (OUTLIER) cc_final: -0.2635 (p0) REVERT: A 326 ILE cc_start: 0.3806 (OUTLIER) cc_final: 0.3509 (mp) REVERT: A 420 ILE cc_start: 0.5312 (OUTLIER) cc_final: 0.4873 (tt) REVERT: B 273 ARG cc_start: 0.6518 (mmt90) cc_final: 0.6252 (mmt90) REVERT: B 443 ILE cc_start: 0.6148 (tt) cc_final: 0.5947 (pp) REVERT: B 475 MET cc_start: 0.7248 (mmp) cc_final: 0.6827 (mmt) REVERT: C 104 MET cc_start: 0.2985 (mmt) cc_final: 0.2627 (tpp) REVERT: C 150 MET cc_start: 0.3568 (mpp) cc_final: 0.3344 (mpp) REVERT: C 166 ARG cc_start: 0.5869 (tmt170) cc_final: 0.3059 (tmt-80) REVERT: D 537 LEU cc_start: 0.3825 (OUTLIER) cc_final: 0.3339 (tt) REVERT: D 591 GLN cc_start: 0.3375 (OUTLIER) cc_final: 0.2855 (mm110) REVERT: D 619 LEU cc_start: 0.3166 (OUTLIER) cc_final: 0.2877 (tm) REVERT: F 626 MET cc_start: 0.1278 (tpp) cc_final: 0.1023 (tpt) REVERT: F 658 GLN cc_start: 0.4868 (OUTLIER) cc_final: 0.4662 (pm20) REVERT: G 51 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6570 (tt) REVERT: L 4 MET cc_start: 0.4612 (mmm) cc_final: 0.2385 (mpt) REVERT: H 71 TYR cc_start: 0.4638 (m-80) cc_final: 0.4416 (m-80) REVERT: H 77 ASN cc_start: 0.7734 (t0) cc_final: 0.7489 (t0) REVERT: H 91 TYR cc_start: 0.7420 (m-80) cc_final: 0.7152 (m-80) REVERT: J 4 MET cc_start: 0.3562 (pmm) cc_final: 0.2859 (ptp) REVERT: J 87 PHE cc_start: 0.1794 (p90) cc_final: 0.1550 (p90) REVERT: J 89 GLN cc_start: 0.3132 (tp40) cc_final: 0.1384 (mt0) outliers start: 106 outliers final: 48 residues processed: 382 average time/residue: 0.4800 time to fit residues: 223.1098 Evaluate side-chains 321 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 12 VAL 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 104 LYS Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 93 VAL 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 44 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 68 PHE 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 20 THR Chi-restraints excluded: chain R residue 87 TYR Chi-restraints excluded: chain R residue 101 GLN Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain C residue 90 THR 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 297 THR 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 D residue 591 GLN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 47 TRP 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 75 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 49 TYR Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 71 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 135 optimal weight: 0.9980 chunk 289 optimal weight: 10.0000 chunk 245 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 192 optimal weight: 0.1980 chunk 218 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 243 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 170 GLN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN F 616 ASN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.161747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.141985 restraints weight = 68640.032| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 3.76 r_work: 0.4111 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4242 moved from start: 1.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 27874 Z= 0.153 Angle : 0.881 13.823 38227 Z= 0.413 Chirality : 0.047 0.408 4749 Planarity : 0.005 0.085 4481 Dihedral : 5.555 38.090 3357 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.73 % Favored : 93.24 % Rotamer: Outliers : 4.13 % Allowed : 31.73 % Favored : 64.13 % 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: -1.65 (0.15), residues: 3031 helix: -0.45 (0.26), residues: 376 sheet: -0.02 (0.17), residues: 941 loop : -1.95 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 178 TYR 0.023 0.002 TYR O 116 PHE 0.036 0.002 PHE K 63 TRP 0.037 0.002 TRP J 67 HIS 0.009 0.001 HIS G 71A Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (27617) covalent geometry : angle 0.84074 / 0.40 (37503) SS BOND : bond 0.00523 / 0.28 ( 47) SS BOND : angle 1.86867 / 1.21 ( 94) hydrogen bonds : bond 0.03795 / 2.50 ( 772) hydrogen bonds : angle 5.98679 / 4.11 ( 2007) link_ALPHA1-2 : bond 0.00466 / 0.29 ( 26) link_ALPHA1-2 : angle 1.52503 / 1.01 ( 78) link_ALPHA1-3 : bond 0.00620 / 0.38 ( 27) link_ALPHA1-3 : angle 1.57571 / 1.00 ( 81) link_ALPHA1-6 : bond 0.00572 / 0.35 ( 24) link_ALPHA1-6 : angle 1.49212 / 0.94 ( 72) link_BETA1-4 : bond 0.00494 / 0.34 ( 69) link_BETA1-4 : angle 1.71787 / 1.18 ( 207) link_NAG-ASN : bond 0.00603 / 0.35 ( 64) link_NAG-ASN : angle 2.97662 / 1.88 ( 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 416 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 305 time to evaluate : 0.793 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 2 MET cc_start: 0.6409 (ttt) cc_final: 0.5674 (ttm) REVERT: O 64 VAL cc_start: 0.5365 (m) cc_final: 0.5102 (m) REVERT: O 81 LEU cc_start: 0.5318 (pp) cc_final: 0.4723 (tp) REVERT: O 119 MET cc_start: 0.3853 (ptm) cc_final: 0.3404 (ptp) REVERT: P 36 TYR cc_start: 0.2921 (OUTLIER) cc_final: 0.2569 (t80) REVERT: P 104 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7036 (tppt) REVERT: P 106 GLU cc_start: 0.7074 (pm20) cc_final: 0.6783 (pm20) REVERT: M 2 MET cc_start: 0.4524 (pmm) cc_final: 0.4323 (pmm) REVERT: M 51 MET cc_start: 0.1689 (mtm) cc_final: 0.0972 (tpp) REVERT: R 4 MET cc_start: 0.0740 (tpp) cc_final: 0.0519 (tpp) REVERT: A 100 MET cc_start: 0.0596 (mtp) cc_final: 0.0057 (tpt) REVERT: A 104 MET cc_start: 0.2179 (mtt) cc_final: 0.1288 (tpt) REVERT: A 247 CYS cc_start: 0.2847 (OUTLIER) cc_final: 0.1988 (p) REVERT: A 271 MET cc_start: 0.0459 (OUTLIER) cc_final: -0.0805 (ppp) REVERT: A 276 ASN cc_start: -0.1207 (OUTLIER) cc_final: -0.2374 (p0) REVERT: A 287 GLN cc_start: 0.5030 (pt0) cc_final: 0.4133 (tp40) REVERT: A 420 ILE cc_start: 0.5324 (OUTLIER) cc_final: 0.5073 (tt) REVERT: B 150 MET cc_start: 0.3391 (pmm) cc_final: 0.2910 (mpp) REVERT: B 443 ILE cc_start: 0.6721 (tt) cc_final: 0.6513 (pp) REVERT: B 475 MET cc_start: 0.7708 (mmp) cc_final: 0.7468 (mmt) REVERT: C 100 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7156 (ptt) REVERT: C 104 MET cc_start: 0.3205 (mmt) cc_final: 0.2905 (tpp) REVERT: C 141 ASP cc_start: 0.4684 (p0) cc_final: 0.4282 (p0) REVERT: C 166 ARG cc_start: 0.5728 (tmt170) cc_final: 0.2668 (tmt-80) REVERT: D 535 MET cc_start: 0.6295 (ttt) cc_final: 0.5995 (ttm) REVERT: D 537 LEU cc_start: 0.3835 (OUTLIER) cc_final: 0.3363 (tt) REVERT: D 591 GLN cc_start: 0.3463 (OUTLIER) cc_final: 0.2808 (mm110) REVERT: D 626 MET cc_start: 0.6332 (ptm) cc_final: 0.5212 (tmt) REVERT: D 635 ILE cc_start: 0.3618 (OUTLIER) cc_final: 0.3407 (tp) REVERT: F 530 MET cc_start: 0.4484 (mpp) cc_final: 0.1795 (pp-130) REVERT: F 658 GLN cc_start: 0.4886 (OUTLIER) cc_final: 0.4532 (pm20) REVERT: K 67 VAL cc_start: 0.6131 (OUTLIER) cc_final: 0.5803 (p) REVERT: G 51 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.6890 (tt) REVERT: G 63 PHE cc_start: 0.5491 (m-80) cc_final: 0.4615 (m-80) REVERT: L 4 MET cc_start: 0.4571 (mmm) cc_final: 0.2381 (mpt) REVERT: L 35 TRP cc_start: 0.1988 (m100) cc_final: 0.1507 (m100) REVERT: H 75 ILE cc_start: 0.4847 (OUTLIER) cc_final: 0.4016 (tt) REVERT: H 77 ASN cc_start: 0.7898 (t0) cc_final: 0.7517 (t0) REVERT: J 4 MET cc_start: 0.3530 (pmm) cc_final: 0.2891 (ptp) REVERT: J 89 GLN cc_start: 0.3536 (tp40) cc_final: 0.1783 (mt0) outliers start: 111 outliers final: 55 residues processed: 385 average time/residue: 0.4324 time to fit residues: 206.3683 Evaluate side-chains 338 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 27 PHE 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 73 LEU Chi-restraints excluded: chain P residue 104 LYS Chi-restraints excluded: chain M residue 93 VAL 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 44 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 68 PHE 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 20 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL 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 258 GLN 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 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 F residue 658 GLN Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 47 TRP 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 96 GLU 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 52 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 190 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 142 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 266 optimal weight: 0.0570 chunk 181 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 1 GLN Q 80 HIS A 105 HIS A 315 GLN ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN C 428 GLN ** F 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN ** G 71AHIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.162659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.142428 restraints weight = 69503.383| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 4.18 r_work: 0.4124 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4579 moved from start: 1.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27874 Z= 0.157 Angle : 0.894 14.917 38227 Z= 0.419 Chirality : 0.049 0.442 4749 Planarity : 0.005 0.076 4481 Dihedral : 5.345 35.312 3357 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.35 % Allowed : 32.92 % Favored : 63.72 % 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: -1.52 (0.15), residues: 3031 helix: -0.37 (0.27), residues: 373 sheet: 0.03 (0.16), residues: 962 loop : -1.86 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 39 TYR 0.024 0.002 TYR H 71 PHE 0.030 0.002 PHE L 87 TRP 0.034 0.002 TRP J 67 HIS 0.009 0.001 HIS G 71A Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (27617) covalent geometry : angle 0.85447 / 0.41 (37503) SS BOND : bond 0.00532 / 0.28 ( 47) SS BOND : angle 1.94430 / 1.27 ( 94) hydrogen bonds : bond 0.03724 / 2.44 ( 772) hydrogen bonds : angle 5.90766 / 4.05 ( 2007) link_ALPHA1-2 : bond 0.00425 / 0.27 ( 26) link_ALPHA1-2 : angle 1.51113 / 1.00 ( 78) link_ALPHA1-3 : bond 0.00587 / 0.37 ( 27) link_ALPHA1-3 : angle 1.61653 / 1.02 ( 81) link_ALPHA1-6 : bond 0.00550 / 0.34 ( 24) link_ALPHA1-6 : angle 1.49773 / 0.93 ( 72) link_BETA1-4 : bond 0.00528 / 0.33 ( 69) link_BETA1-4 : angle 1.71909 / 1.19 ( 207) link_NAG-ASN : bond 0.00580 / 0.33 ( 64) link_NAG-ASN : angle 2.92435 / 1.88 ( 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 412 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 322 time to evaluate : 0.901 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: 0.6733 (ttt) cc_final: 0.5971 (ttm) REVERT: O 51 MET cc_start: 0.6920 (mpp) cc_final: 0.6562 (mtp) REVERT: O 64 VAL cc_start: 0.5511 (m) cc_final: 0.5235 (m) REVERT: O 81 LEU cc_start: 0.5391 (pp) cc_final: 0.4918 (tp) REVERT: P 104 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7078 (tppt) REVERT: P 106 GLU cc_start: 0.7325 (pm20) cc_final: 0.6958 (pm20) REVERT: M 2 MET cc_start: 0.4532 (pmm) cc_final: 0.4312 (pmm) REVERT: M 34 MET cc_start: 0.0122 (ttt) cc_final: -0.0427 (ttp) REVERT: M 51 MET cc_start: 0.1775 (mtm) cc_final: 0.0932 (mmm) REVERT: M 83 MET cc_start: 0.0909 (mpt) cc_final: -0.0624 (tmm) REVERT: R 4 MET cc_start: 0.0970 (tpp) cc_final: 0.0738 (tpp) REVERT: R 104 LYS cc_start: 0.5536 (tptp) cc_final: 0.4997 (mmmt) REVERT: A 100 MET cc_start: 0.0727 (mtp) cc_final: 0.0269 (mmt) REVERT: A 104 MET cc_start: 0.2273 (mtt) cc_final: 0.1370 (tpt) REVERT: A 247 CYS cc_start: 0.2978 (OUTLIER) cc_final: 0.2035 (p) REVERT: A 271 MET cc_start: 0.0604 (OUTLIER) cc_final: 0.0382 (ppp) REVERT: A 276 ASN cc_start: -0.1254 (OUTLIER) cc_final: -0.2315 (p0) REVERT: A 287 GLN cc_start: 0.5356 (pt0) cc_final: 0.4497 (pt0) REVERT: A 420 ILE cc_start: 0.5383 (OUTLIER) cc_final: 0.5160 (tt) REVERT: B 166 ARG cc_start: 0.6623 (mmt-90) cc_final: 0.6347 (tpt-90) REVERT: C 104 MET cc_start: 0.3582 (mmt) cc_final: 0.3326 (tpp) REVERT: C 141 ASP cc_start: 0.5158 (p0) cc_final: 0.4686 (p0) REVERT: C 150 MET cc_start: 0.3798 (OUTLIER) cc_final: 0.3586 (mpp) REVERT: C 166 ARG cc_start: 0.5907 (tmt170) cc_final: 0.3374 (tmt-80) REVERT: C 426 MET cc_start: 0.3242 (ptm) cc_final: 0.3013 (ptp) REVERT: D 535 MET cc_start: 0.6315 (ttt) cc_final: 0.6014 (ttm) REVERT: D 537 LEU cc_start: 0.4034 (OUTLIER) cc_final: 0.3651 (tt) REVERT: D 591 GLN cc_start: 0.3392 (OUTLIER) cc_final: 0.2885 (mm110) REVERT: D 619 LEU cc_start: 0.3238 (OUTLIER) cc_final: 0.2950 (tm) REVERT: D 626 MET cc_start: 0.6344 (ptm) cc_final: 0.5167 (tmt) REVERT: F 530 MET cc_start: 0.4618 (mpp) cc_final: 0.1490 (pp-130) REVERT: F 601 LYS cc_start: 0.5511 (tppp) cc_final: 0.4005 (ttpt) REVERT: F 638 TYR cc_start: 0.4561 (m-80) cc_final: 0.4081 (m-80) REVERT: F 658 GLN cc_start: 0.4837 (OUTLIER) cc_final: 0.4580 (pm20) REVERT: K 82 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.3976 (mptt) REVERT: G 51 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7373 (tt) REVERT: G 80 MET cc_start: 0.6053 (ppp) cc_final: 0.5641 (ptm) REVERT: L 35 TRP cc_start: 0.2260 (m100) cc_final: 0.1852 (m100) REVERT: H 77 ASN cc_start: 0.7825 (t0) cc_final: 0.7508 (t0) REVERT: J 87 PHE cc_start: 0.1719 (p90) cc_final: 0.1342 (p90) REVERT: J 89 GLN cc_start: 0.3615 (tp40) cc_final: 0.1916 (mt0) outliers start: 90 outliers final: 50 residues processed: 383 average time/residue: 0.4385 time to fit residues: 208.8428 Evaluate side-chains 339 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 69 THR Chi-restraints excluded: chain P residue 20 THR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 104 LYS Chi-restraints excluded: chain M residue 93 VAL 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 44 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 68 PHE 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 20 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 271 MET 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 420 ILE 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 255 VAL Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 150 MET 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 292 VAL 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 D residue 591 GLN Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 47 TRP 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 J residue 2 ILE Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 249 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 chunk 129 optimal weight: 0.0770 chunk 2 optimal weight: 10.0000 chunk 140 optimal weight: 0.3980 chunk 6 optimal weight: 0.0030 chunk 151 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 121 optimal weight: 0.0070 overall best weight: 0.2766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Q 80 HIS A 105 HIS ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 GLN C 428 GLN F 616 ASN I 59 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.163075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.142864 restraints weight = 69511.589| |-----------------------------------------------------------------------------| r_work (start): 0.4218 rms_B_bonded: 4.26 r_work: 0.4119 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4604 moved from start: 1.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27874 Z= 0.140 Angle : 0.892 23.097 38227 Z= 0.412 Chirality : 0.047 0.399 4749 Planarity : 0.005 0.072 4481 Dihedral : 5.194 32.534 3357 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.72 % Allowed : 34.23 % Favored : 63.05 % 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: -1.45 (0.15), residues: 3031 helix: -0.35 (0.27), residues: 373 sheet: 0.10 (0.16), residues: 971 loop : -1.82 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 83 TYR 0.026 0.002 TYR O 116 PHE 0.034 0.002 PHE Q 27 TRP 0.049 0.002 TRP A 35 HIS 0.009 0.001 HIS G 71A Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (27617) covalent geometry : angle 0.84240 / 0.40 (37503) SS BOND : bond 0.00490 / 0.26 ( 47) SS BOND : angle 1.71072 / 1.14 ( 94) hydrogen bonds : bond 0.03626 / 2.36 ( 772) hydrogen bonds : angle 5.71073 / 3.91 ( 2007) link_ALPHA1-2 : bond 0.00490 / 0.31 ( 26) link_ALPHA1-2 : angle 1.48704 / 0.97 ( 78) link_ALPHA1-3 : bond 0.00601 / 0.37 ( 27) link_ALPHA1-3 : angle 1.59359 / 1.01 ( 81) link_ALPHA1-6 : bond 0.00545 / 0.33 ( 24) link_ALPHA1-6 : angle 1.44533 / 0.91 ( 72) link_BETA1-4 : bond 0.00492 / 0.33 ( 69) link_BETA1-4 : angle 1.64442 / 1.13 ( 207) link_NAG-ASN : bond 0.00619 / 0.32 ( 64) link_NAG-ASN : angle 3.56659 / 2.47 ( 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 370 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 297 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 2 MET cc_start: 0.6945 (ttt) cc_final: 0.6426 (ttm) REVERT: O 51 MET cc_start: 0.6892 (mpp) cc_final: 0.6486 (mtp) REVERT: O 64 VAL cc_start: 0.5447 (m) cc_final: 0.5152 (m) REVERT: O 81 LEU cc_start: 0.5282 (pp) cc_final: 0.4899 (tp) REVERT: O 84 ASP cc_start: 0.7587 (m-30) cc_final: 0.6898 (p0) REVERT: O 119 MET cc_start: 0.3823 (ptm) cc_final: 0.3362 (ptp) REVERT: P 18 ARG cc_start: 0.6987 (ttm-80) cc_final: 0.6652 (ttm170) REVERT: P 36 TYR cc_start: 0.3252 (OUTLIER) cc_final: 0.2820 (t80) REVERT: P 104 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7071 (tppt) REVERT: P 106 GLU cc_start: 0.7404 (pm20) cc_final: 0.7136 (pm20) REVERT: M 34 MET cc_start: 0.0122 (ttt) cc_final: -0.0464 (ttp) REVERT: M 51 MET cc_start: 0.1667 (mtm) cc_final: 0.0840 (mmm) REVERT: R 4 MET cc_start: 0.1315 (tpp) cc_final: 0.1112 (tpp) REVERT: R 104 LYS cc_start: 0.5534 (tptp) cc_final: 0.5005 (mmmt) REVERT: A 100 MET cc_start: 0.0966 (mtp) cc_final: 0.0743 (mmm) REVERT: A 104 MET cc_start: 0.2284 (mtt) cc_final: 0.1536 (tpt) REVERT: A 247 CYS cc_start: 0.2695 (OUTLIER) cc_final: 0.1677 (p) REVERT: A 271 MET cc_start: 0.0447 (OUTLIER) cc_final: -0.0695 (ppp) REVERT: A 276 ASN cc_start: -0.1105 (OUTLIER) cc_final: -0.2098 (p0) REVERT: A 287 GLN cc_start: 0.5265 (pt0) cc_final: 0.4195 (tp40) REVERT: B 66 HIS cc_start: 0.4274 (OUTLIER) cc_final: 0.3834 (p90) REVERT: B 100 MET cc_start: 0.4264 (pp-130) cc_final: 0.3896 (ppp) REVERT: B 255 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8518 (t) REVERT: C 104 MET cc_start: 0.3781 (mmt) cc_final: 0.3572 (tpp) REVERT: C 141 ASP cc_start: 0.5361 (p0) cc_final: 0.4907 (p0) REVERT: C 166 ARG cc_start: 0.5954 (tmt170) cc_final: 0.3402 (tmt-80) REVERT: D 535 MET cc_start: 0.6278 (ttt) cc_final: 0.6000 (ttm) REVERT: D 537 LEU cc_start: 0.4027 (OUTLIER) cc_final: 0.3738 (tt) REVERT: D 619 LEU cc_start: 0.3432 (OUTLIER) cc_final: 0.3154 (tm) REVERT: D 626 MET cc_start: 0.6195 (ptm) cc_final: 0.5115 (tmt) REVERT: F 530 MET cc_start: 0.4580 (mpp) cc_final: 0.1611 (pp-130) REVERT: F 601 LYS cc_start: 0.5337 (tppp) cc_final: 0.3837 (ttpt) REVERT: F 658 GLN cc_start: 0.4839 (OUTLIER) cc_final: 0.4489 (pm20) REVERT: G 51 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7393 (tt) REVERT: G 80 MET cc_start: 0.6012 (ppp) cc_final: 0.5679 (ptm) REVERT: G 94 ARG cc_start: 0.8081 (ptm-80) cc_final: 0.7850 (mtm180) REVERT: I 34 ILE cc_start: 0.0423 (OUTLIER) cc_final: -0.0167 (pt) REVERT: L 4 MET cc_start: 0.3654 (mpt) cc_final: 0.3000 (mpt) REVERT: L 36 TYR cc_start: 0.2847 (m-10) cc_final: 0.1075 (m-10) REVERT: H 77 ASN cc_start: 0.8027 (t0) cc_final: 0.7624 (t0) REVERT: J 87 PHE cc_start: 0.2003 (p90) cc_final: 0.1702 (p90) REVERT: J 89 GLN cc_start: 0.3316 (tp40) cc_final: 0.1559 (mt0) outliers start: 73 outliers final: 44 residues processed: 349 average time/residue: 0.4303 time to fit residues: 185.5518 Evaluate side-chains 333 residues out of total 2688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 79 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 73 LEU Chi-restraints excluded: chain P residue 104 LYS Chi-restraints excluded: chain M residue 114 TYR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 68 PHE 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 20 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain C residue 90 THR 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 455 THR Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain E residue 658 GLN Chi-restraints excluded: chain F residue 658 GLN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 47 TRP Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain L residue 83 ILE 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 J residue 2 ILE Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain J residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 179 optimal weight: 0.8980 chunk 72 optimal weight: 0.2980 chunk 293 optimal weight: 0.7980 chunk 189 optimal weight: 6.9990 chunk 205 optimal weight: 0.0040 chunk 49 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 166 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 270 optimal weight: 8.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS A 195 ASN A 377 ASN B 249 HIS ** C 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.164294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.143879 restraints weight = 69137.134| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 3.90 r_work: 0.4131 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4792 moved from start: 1.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 27874 Z= 0.148 Angle : 0.891 22.301 38227 Z= 0.412 Chirality : 0.047 0.374 4749 Planarity : 0.005 0.088 4481 Dihedral : 5.142 28.676 3357 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.35 % Allowed : 35.27 % Favored : 62.38 % 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: -1.39 (0.15), residues: 3031 helix: -0.32 (0.26), residues: 372 sheet: 0.13 (0.16), residues: 989 loop : -1.79 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 588 TYR 0.030 0.002 TYR D 643 PHE 0.029 0.002 PHE L 87 TRP 0.035 0.002 TRP J 67 HIS 0.009 0.001 HIS G 71A Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (27617) covalent geometry : angle 0.84565 / 0.40 (37503) SS BOND : bond 0.00548 / 0.32 ( 47) SS BOND : angle 1.70402 / 1.13 ( 94) hydrogen bonds : bond 0.03692 / 2.45 ( 772) hydrogen bonds : angle 5.71686 / 3.92 ( 2007) link_ALPHA1-2 : bond 0.00523 / 0.35 ( 26) link_ALPHA1-2 : angle 1.52816 / 0.99 ( 78) link_ALPHA1-3 : bond 0.00579 / 0.35 ( 27) link_ALPHA1-3 : angle 1.58324 / 1.00 ( 81) link_ALPHA1-6 : bond 0.00514 / 0.32 ( 24) link_ALPHA1-6 : angle 1.43918 / 0.91 ( 72) link_BETA1-4 : bond 0.00510 / 0.34 ( 69) link_BETA1-4 : angle 1.60714 / 1.10 ( 207) link_NAG-ASN : bond 0.00631 / 0.33 ( 64) link_NAG-ASN : angle 3.35128 / 2.30 ( 192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9529.42 seconds wall clock time: 163 minutes 18.47 seconds (9798.47 seconds total)