Starting phenix.real_space_refine on Sun Dec 29 23:24:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xm1_33289/12_2024/7xm1_33289.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xm1_33289/12_2024/7xm1_33289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xm1_33289/12_2024/7xm1_33289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xm1_33289/12_2024/7xm1_33289.map" model { file = "/net/cci-nas-00/data/ceres_data/7xm1_33289/12_2024/7xm1_33289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xm1_33289/12_2024/7xm1_33289.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians Ba 60 18.26 5 S 180 5.16 5 C 37800 2.51 5 N 10080 2.21 5 O 12120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 60240 Number of models: 1 Model: "" Number of chains: 101 Chain: "A" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "B" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "G" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "I" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "J" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "K" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "L" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "M" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "N" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "O" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "P" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "Q" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "R" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "S" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "T" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "V" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "W" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "X" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "Y" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "Z" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "AA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "BA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "CA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "DA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "EA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "FA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "GA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "HA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "IA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "JA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "KA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "LA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "MA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "NA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "OA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "PA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "QA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "RA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "SA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "TA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "UA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "VA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "WA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "XA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "YA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "ZA" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "AB" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "BB" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "CB" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "DB" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "EB" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "FB" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "GB" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "HB" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "IB" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1003 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "DA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "EA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "FA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "GA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "IA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "JA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "KA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "LA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "MA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "OA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "QA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "TA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "BB" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "DB" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "EB" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' BA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "FB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "GB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "HB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Chain: "IB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' BA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 24.72, per 1000 atoms: 0.41 Number of scatterers: 60240 At special positions: 0 Unit cell: (215.6, 215.6, 215.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ba 60 55.98 S 180 16.00 O 12120 8.00 N 10080 7.00 C 37800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 11.53 Conformation dependent library (CDL) restraints added in 5.7 seconds 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14400 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 120 sheets defined 48.8% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.80 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLU B 90 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 132 Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 132 Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU F 90 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 132 Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU G 90 " --> pdb=" O THR G 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 132 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLU H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 132 Processing helix chain 'I' and resid 64 through 66 No H-bonds generated for 'chain 'I' and resid 64 through 66' Processing helix chain 'I' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER I 117 " --> pdb=" O GLN I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 132 Processing helix chain 'J' and resid 64 through 66 No H-bonds generated for 'chain 'J' and resid 64 through 66' Processing helix chain 'J' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLU J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 132 Processing helix chain 'K' and resid 64 through 66 No H-bonds generated for 'chain 'K' and resid 64 through 66' Processing helix chain 'K' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLU K 90 " --> pdb=" O THR K 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER K 117 " --> pdb=" O GLN K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 132 Processing helix chain 'L' and resid 64 through 66 No H-bonds generated for 'chain 'L' and resid 64 through 66' Processing helix chain 'L' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLU L 90 " --> pdb=" O THR L 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER L 117 " --> pdb=" O GLN L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 132 Processing helix chain 'M' and resid 64 through 66 No H-bonds generated for 'chain 'M' and resid 64 through 66' Processing helix chain 'M' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU M 90 " --> pdb=" O THR M 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 132 Processing helix chain 'N' and resid 64 through 66 No H-bonds generated for 'chain 'N' and resid 64 through 66' Processing helix chain 'N' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU N 90 " --> pdb=" O THR N 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 132 Processing helix chain 'O' and resid 64 through 66 No H-bonds generated for 'chain 'O' and resid 64 through 66' Processing helix chain 'O' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU O 90 " --> pdb=" O THR O 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 132 Processing helix chain 'P' and resid 64 through 66 No H-bonds generated for 'chain 'P' and resid 64 through 66' Processing helix chain 'P' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU P 90 " --> pdb=" O THR P 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 132 Processing helix chain 'Q' and resid 64 through 66 No H-bonds generated for 'chain 'Q' and resid 64 through 66' Processing helix chain 'Q' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU Q 90 " --> pdb=" O THR Q 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 132 Processing helix chain 'R' and resid 64 through 66 No H-bonds generated for 'chain 'R' and resid 64 through 66' Processing helix chain 'R' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU R 90 " --> pdb=" O THR R 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 132 Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLU S 90 " --> pdb=" O THR S 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER S 117 " --> pdb=" O GLN S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 132 Processing helix chain 'T' and resid 64 through 66 No H-bonds generated for 'chain 'T' and resid 64 through 66' Processing helix chain 'T' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU T 90 " --> pdb=" O THR T 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER T 117 " --> pdb=" O GLN T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 132 Processing helix chain 'V' and resid 64 through 66 No H-bonds generated for 'chain 'V' and resid 64 through 66' Processing helix chain 'V' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU V 90 " --> pdb=" O THR V 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER V 117 " --> pdb=" O GLN V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 132 Processing helix chain 'W' and resid 64 through 66 No H-bonds generated for 'chain 'W' and resid 64 through 66' Processing helix chain 'W' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU W 90 " --> pdb=" O THR W 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER W 117 " --> pdb=" O GLN W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 Processing helix chain 'X' and resid 64 through 66 No H-bonds generated for 'chain 'X' and resid 64 through 66' Processing helix chain 'X' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLU X 90 " --> pdb=" O THR X 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 119 through 132 Processing helix chain 'Y' and resid 64 through 66 No H-bonds generated for 'chain 'Y' and resid 64 through 66' Processing helix chain 'Y' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU Y 90 " --> pdb=" O THR Y 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER Y 117 " --> pdb=" O GLN Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 132 Processing helix chain 'Z' and resid 64 through 66 No H-bonds generated for 'chain 'Z' and resid 64 through 66' Processing helix chain 'Z' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLU Z 90 " --> pdb=" O THR Z 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER Z 117 " --> pdb=" O GLN Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 119 through 132 Processing helix chain 'AA' and resid 64 through 66 No H-bonds generated for 'chain 'AA' and resid 64 through 66' Processing helix chain 'AA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUAA 90 " --> pdb=" O THRAA 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERAA 117 " --> pdb=" O GLNAA 113 " (cutoff:3.500A) Processing helix chain 'AA' and resid 119 through 132 Processing helix chain 'BA' and resid 64 through 66 No H-bonds generated for 'chain 'BA' and resid 64 through 66' Processing helix chain 'BA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUBA 90 " --> pdb=" O THRBA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERBA 117 " --> pdb=" O GLNBA 113 " (cutoff:3.500A) Processing helix chain 'BA' and resid 119 through 132 Processing helix chain 'CA' and resid 64 through 66 No H-bonds generated for 'chain 'CA' and resid 64 through 66' Processing helix chain 'CA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUCA 90 " --> pdb=" O THRCA 86 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SERCA 117 " --> pdb=" O GLNCA 113 " (cutoff:3.500A) Processing helix chain 'CA' and resid 119 through 132 Processing helix chain 'DA' and resid 64 through 66 No H-bonds generated for 'chain 'DA' and resid 64 through 66' Processing helix chain 'DA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUDA 90 " --> pdb=" O THRDA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERDA 117 " --> pdb=" O GLNDA 113 " (cutoff:3.500A) Processing helix chain 'DA' and resid 119 through 132 Processing helix chain 'EA' and resid 64 through 66 No H-bonds generated for 'chain 'EA' and resid 64 through 66' Processing helix chain 'EA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUEA 90 " --> pdb=" O THREA 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SEREA 117 " --> pdb=" O GLNEA 113 " (cutoff:3.500A) Processing helix chain 'EA' and resid 119 through 132 Processing helix chain 'FA' and resid 64 through 66 No H-bonds generated for 'chain 'FA' and resid 64 through 66' Processing helix chain 'FA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUFA 90 " --> pdb=" O THRFA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERFA 117 " --> pdb=" O GLNFA 113 " (cutoff:3.500A) Processing helix chain 'FA' and resid 119 through 132 Processing helix chain 'GA' and resid 64 through 66 No H-bonds generated for 'chain 'GA' and resid 64 through 66' Processing helix chain 'GA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUGA 90 " --> pdb=" O THRGA 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERGA 117 " --> pdb=" O GLNGA 113 " (cutoff:3.500A) Processing helix chain 'GA' and resid 119 through 132 Processing helix chain 'HA' and resid 64 through 66 No H-bonds generated for 'chain 'HA' and resid 64 through 66' Processing helix chain 'HA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUHA 90 " --> pdb=" O THRHA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERHA 117 " --> pdb=" O GLNHA 113 " (cutoff:3.500A) Processing helix chain 'HA' and resid 119 through 132 Processing helix chain 'IA' and resid 64 through 66 No H-bonds generated for 'chain 'IA' and resid 64 through 66' Processing helix chain 'IA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUIA 90 " --> pdb=" O THRIA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERIA 117 " --> pdb=" O GLNIA 113 " (cutoff:3.500A) Processing helix chain 'IA' and resid 119 through 132 Processing helix chain 'JA' and resid 64 through 66 No H-bonds generated for 'chain 'JA' and resid 64 through 66' Processing helix chain 'JA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUJA 90 " --> pdb=" O THRJA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERJA 117 " --> pdb=" O GLNJA 113 " (cutoff:3.500A) Processing helix chain 'JA' and resid 119 through 132 Processing helix chain 'KA' and resid 64 through 66 No H-bonds generated for 'chain 'KA' and resid 64 through 66' Processing helix chain 'KA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUKA 90 " --> pdb=" O THRKA 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERKA 117 " --> pdb=" O GLNKA 113 " (cutoff:3.500A) Processing helix chain 'KA' and resid 119 through 132 Processing helix chain 'LA' and resid 64 through 66 No H-bonds generated for 'chain 'LA' and resid 64 through 66' Processing helix chain 'LA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLULA 90 " --> pdb=" O THRLA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERLA 117 " --> pdb=" O GLNLA 113 " (cutoff:3.500A) Processing helix chain 'LA' and resid 119 through 132 Processing helix chain 'MA' and resid 64 through 66 No H-bonds generated for 'chain 'MA' and resid 64 through 66' Processing helix chain 'MA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUMA 90 " --> pdb=" O THRMA 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERMA 117 " --> pdb=" O GLNMA 113 " (cutoff:3.500A) Processing helix chain 'MA' and resid 119 through 132 Processing helix chain 'NA' and resid 64 through 66 No H-bonds generated for 'chain 'NA' and resid 64 through 66' Processing helix chain 'NA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUNA 90 " --> pdb=" O THRNA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERNA 117 " --> pdb=" O GLNNA 113 " (cutoff:3.500A) Processing helix chain 'NA' and resid 119 through 132 Processing helix chain 'OA' and resid 64 through 66 No H-bonds generated for 'chain 'OA' and resid 64 through 66' Processing helix chain 'OA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUOA 90 " --> pdb=" O THROA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SEROA 117 " --> pdb=" O GLNOA 113 " (cutoff:3.500A) Processing helix chain 'OA' and resid 119 through 132 Processing helix chain 'PA' and resid 64 through 66 No H-bonds generated for 'chain 'PA' and resid 64 through 66' Processing helix chain 'PA' and resid 75 through 117 removed outlier: 3.737A pdb=" N GLUPA 90 " --> pdb=" O THRPA 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERPA 117 " --> pdb=" O GLNPA 113 " (cutoff:3.500A) Processing helix chain 'PA' and resid 119 through 132 Processing helix chain 'QA' and resid 64 through 66 No H-bonds generated for 'chain 'QA' and resid 64 through 66' Processing helix chain 'QA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUQA 90 " --> pdb=" O THRQA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERQA 117 " --> pdb=" O GLNQA 113 " (cutoff:3.500A) Processing helix chain 'QA' and resid 119 through 132 Processing helix chain 'RA' and resid 64 through 66 No H-bonds generated for 'chain 'RA' and resid 64 through 66' Processing helix chain 'RA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLURA 90 " --> pdb=" O THRRA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERRA 117 " --> pdb=" O GLNRA 113 " (cutoff:3.500A) Processing helix chain 'RA' and resid 119 through 132 Processing helix chain 'SA' and resid 64 through 66 No H-bonds generated for 'chain 'SA' and resid 64 through 66' Processing helix chain 'SA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUSA 90 " --> pdb=" O THRSA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERSA 117 " --> pdb=" O GLNSA 113 " (cutoff:3.500A) Processing helix chain 'SA' and resid 119 through 132 Processing helix chain 'TA' and resid 64 through 66 No H-bonds generated for 'chain 'TA' and resid 64 through 66' Processing helix chain 'TA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUTA 90 " --> pdb=" O THRTA 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERTA 117 " --> pdb=" O GLNTA 113 " (cutoff:3.500A) Processing helix chain 'TA' and resid 119 through 132 Processing helix chain 'UA' and resid 64 through 66 No H-bonds generated for 'chain 'UA' and resid 64 through 66' Processing helix chain 'UA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUUA 90 " --> pdb=" O THRUA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERUA 117 " --> pdb=" O GLNUA 113 " (cutoff:3.500A) Processing helix chain 'UA' and resid 119 through 132 Processing helix chain 'VA' and resid 64 through 66 No H-bonds generated for 'chain 'VA' and resid 64 through 66' Processing helix chain 'VA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUVA 90 " --> pdb=" O THRVA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERVA 117 " --> pdb=" O GLNVA 113 " (cutoff:3.500A) Processing helix chain 'VA' and resid 119 through 132 Processing helix chain 'WA' and resid 64 through 66 No H-bonds generated for 'chain 'WA' and resid 64 through 66' Processing helix chain 'WA' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUWA 90 " --> pdb=" O THRWA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERWA 117 " --> pdb=" O GLNWA 113 " (cutoff:3.500A) Processing helix chain 'WA' and resid 119 through 132 Processing helix chain 'XA' and resid 64 through 66 No H-bonds generated for 'chain 'XA' and resid 64 through 66' Processing helix chain 'XA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUXA 90 " --> pdb=" O THRXA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERXA 117 " --> pdb=" O GLNXA 113 " (cutoff:3.500A) Processing helix chain 'XA' and resid 119 through 132 Processing helix chain 'YA' and resid 64 through 66 No H-bonds generated for 'chain 'YA' and resid 64 through 66' Processing helix chain 'YA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUYA 90 " --> pdb=" O THRYA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERYA 117 " --> pdb=" O GLNYA 113 " (cutoff:3.500A) Processing helix chain 'YA' and resid 119 through 132 Processing helix chain 'ZA' and resid 64 through 66 No H-bonds generated for 'chain 'ZA' and resid 64 through 66' Processing helix chain 'ZA' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUZA 90 " --> pdb=" O THRZA 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERZA 117 " --> pdb=" O GLNZA 113 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 119 through 132 Processing helix chain 'AB' and resid 64 through 66 No H-bonds generated for 'chain 'AB' and resid 64 through 66' Processing helix chain 'AB' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUAB 90 " --> pdb=" O THRAB 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERAB 117 " --> pdb=" O GLNAB 113 " (cutoff:3.500A) Processing helix chain 'AB' and resid 119 through 132 Processing helix chain 'BB' and resid 64 through 66 No H-bonds generated for 'chain 'BB' and resid 64 through 66' Processing helix chain 'BB' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUBB 90 " --> pdb=" O THRBB 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERBB 117 " --> pdb=" O GLNBB 113 " (cutoff:3.500A) Processing helix chain 'BB' and resid 119 through 132 Processing helix chain 'CB' and resid 64 through 66 No H-bonds generated for 'chain 'CB' and resid 64 through 66' Processing helix chain 'CB' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUCB 90 " --> pdb=" O THRCB 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERCB 117 " --> pdb=" O GLNCB 113 " (cutoff:3.500A) Processing helix chain 'CB' and resid 119 through 132 Processing helix chain 'DB' and resid 64 through 66 No H-bonds generated for 'chain 'DB' and resid 64 through 66' Processing helix chain 'DB' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUDB 90 " --> pdb=" O THRDB 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERDB 117 " --> pdb=" O GLNDB 113 " (cutoff:3.500A) Processing helix chain 'DB' and resid 119 through 132 Processing helix chain 'EB' and resid 64 through 66 No H-bonds generated for 'chain 'EB' and resid 64 through 66' Processing helix chain 'EB' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUEB 90 " --> pdb=" O THREB 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SEREB 117 " --> pdb=" O GLNEB 113 " (cutoff:3.500A) Processing helix chain 'EB' and resid 119 through 132 Processing helix chain 'FB' and resid 64 through 66 No H-bonds generated for 'chain 'FB' and resid 64 through 66' Processing helix chain 'FB' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUFB 90 " --> pdb=" O THRFB 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERFB 117 " --> pdb=" O GLNFB 113 " (cutoff:3.500A) Processing helix chain 'FB' and resid 119 through 132 Processing helix chain 'GB' and resid 64 through 66 No H-bonds generated for 'chain 'GB' and resid 64 through 66' Processing helix chain 'GB' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUGB 90 " --> pdb=" O THRGB 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERGB 117 " --> pdb=" O GLNGB 113 " (cutoff:3.500A) Processing helix chain 'GB' and resid 119 through 132 Processing helix chain 'HB' and resid 64 through 66 No H-bonds generated for 'chain 'HB' and resid 64 through 66' Processing helix chain 'HB' and resid 75 through 117 removed outlier: 3.735A pdb=" N GLUHB 90 " --> pdb=" O THRHB 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SERHB 117 " --> pdb=" O GLNHB 113 " (cutoff:3.500A) Processing helix chain 'HB' and resid 119 through 132 Processing helix chain 'IB' and resid 64 through 66 No H-bonds generated for 'chain 'IB' and resid 64 through 66' Processing helix chain 'IB' and resid 75 through 117 removed outlier: 3.736A pdb=" N GLUIB 90 " --> pdb=" O THRIB 86 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SERIB 117 " --> pdb=" O GLNIB 113 " (cutoff:3.500A) Processing helix chain 'IB' and resid 119 through 132 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL A 48 " --> pdb=" O ILE A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL A 48 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA A 31 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 16 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL A 33 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP A 14 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE A 6 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE A 71 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG A 8 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL B 48 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL B 48 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA B 31 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 16 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL B 33 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP B 14 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 6 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE B 71 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG B 8 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL C 48 " --> pdb=" O ILE C 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL C 48 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA C 31 " --> pdb=" O ILE C 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 16 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL C 33 " --> pdb=" O ASP C 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP C 14 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 6 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE C 71 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG C 8 " --> pdb=" O ILE C 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL D 48 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL D 48 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA D 31 " --> pdb=" O ILE D 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D 16 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL D 33 " --> pdb=" O ASP D 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP D 14 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE D 6 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE D 71 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG D 8 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL E 48 " --> pdb=" O ILE E 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL E 48 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA E 31 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE E 16 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL E 33 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP E 14 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE E 6 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE E 71 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG E 8 " --> pdb=" O ILE E 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL F 48 " --> pdb=" O ILE F 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL F 48 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA F 31 " --> pdb=" O ILE F 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE F 16 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL F 33 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP F 14 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE F 6 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE F 71 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG F 8 " --> pdb=" O ILE F 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL G 48 " --> pdb=" O ILE G 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL G 48 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA G 31 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE G 16 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL G 33 " --> pdb=" O ASP G 14 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP G 14 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE G 6 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE G 71 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG G 8 " --> pdb=" O ILE G 69 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL H 48 " --> pdb=" O ILE H 35 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL H 48 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA H 31 " --> pdb=" O ILE H 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE H 16 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL H 33 " --> pdb=" O ASP H 14 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP H 14 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE H 6 " --> pdb=" O ILE H 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE H 71 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG H 8 " --> pdb=" O ILE H 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL I 48 " --> pdb=" O ILE I 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL I 48 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA I 31 " --> pdb=" O ILE I 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE I 16 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL I 33 " --> pdb=" O ASP I 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP I 14 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE I 6 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE I 71 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARG I 8 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL J 48 " --> pdb=" O ILE J 35 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL J 48 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA J 31 " --> pdb=" O ILE J 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE J 16 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL J 33 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP J 14 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE J 6 " --> pdb=" O ILE J 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE J 71 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG J 8 " --> pdb=" O ILE J 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL K 48 " --> pdb=" O ILE K 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL K 48 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA K 31 " --> pdb=" O ILE K 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE K 16 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL K 33 " --> pdb=" O ASP K 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP K 14 " --> pdb=" O VAL K 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE K 6 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE K 71 " --> pdb=" O ILE K 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG K 8 " --> pdb=" O ILE K 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL L 48 " --> pdb=" O ILE L 35 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL L 48 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA L 31 " --> pdb=" O ILE L 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE L 16 " --> pdb=" O ALA L 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL L 33 " --> pdb=" O ASP L 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP L 14 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE L 6 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE L 71 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG L 8 " --> pdb=" O ILE L 69 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL M 48 " --> pdb=" O ILE M 35 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL M 48 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA M 31 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE M 16 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL M 33 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP M 14 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE M 6 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE M 71 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG M 8 " --> pdb=" O ILE M 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 48 through 51 removed outlier: 3.825A pdb=" N VAL N 48 " --> pdb=" O ILE N 35 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 48 through 51 removed outlier: 3.825A pdb=" N VAL N 48 " --> pdb=" O ILE N 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA N 31 " --> pdb=" O ILE N 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE N 16 " --> pdb=" O ALA N 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL N 33 " --> pdb=" O ASP N 14 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP N 14 " --> pdb=" O VAL N 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE N 6 " --> pdb=" O ILE N 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE N 71 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG N 8 " --> pdb=" O ILE N 69 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL O 48 " --> pdb=" O ILE O 35 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL O 48 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA O 31 " --> pdb=" O ILE O 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE O 16 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL O 33 " --> pdb=" O ASP O 14 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP O 14 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE O 6 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE O 71 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG O 8 " --> pdb=" O ILE O 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL P 48 " --> pdb=" O ILE P 35 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL P 48 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA P 31 " --> pdb=" O ILE P 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE P 16 " --> pdb=" O ALA P 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL P 33 " --> pdb=" O ASP P 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP P 14 " --> pdb=" O VAL P 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE P 6 " --> pdb=" O ILE P 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE P 71 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG P 8 " --> pdb=" O ILE P 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL Q 48 " --> pdb=" O ILE Q 35 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL Q 48 " --> pdb=" O ILE Q 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA Q 31 " --> pdb=" O ILE Q 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE Q 16 " --> pdb=" O ALA Q 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL Q 33 " --> pdb=" O ASP Q 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP Q 14 " --> pdb=" O VAL Q 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE Q 6 " --> pdb=" O ILE Q 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE Q 71 " --> pdb=" O ILE Q 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG Q 8 " --> pdb=" O ILE Q 69 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL R 48 " --> pdb=" O ILE R 35 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL R 48 " --> pdb=" O ILE R 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA R 31 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE R 16 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL R 33 " --> pdb=" O ASP R 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP R 14 " --> pdb=" O VAL R 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE R 6 " --> pdb=" O ILE R 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE R 71 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG R 8 " --> pdb=" O ILE R 69 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 48 through 51 removed outlier: 3.825A pdb=" N VAL S 48 " --> pdb=" O ILE S 35 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 48 through 51 removed outlier: 3.825A pdb=" N VAL S 48 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA S 31 " --> pdb=" O ILE S 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE S 16 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL S 33 " --> pdb=" O ASP S 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP S 14 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE S 6 " --> pdb=" O ILE S 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE S 71 " --> pdb=" O ILE S 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG S 8 " --> pdb=" O ILE S 69 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 48 through 51 removed outlier: 3.825A pdb=" N VAL T 48 " --> pdb=" O ILE T 35 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 48 through 51 removed outlier: 3.825A pdb=" N VAL T 48 " --> pdb=" O ILE T 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA T 31 " --> pdb=" O ILE T 16 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE T 16 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL T 33 " --> pdb=" O ASP T 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP T 14 " --> pdb=" O VAL T 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE T 6 " --> pdb=" O ILE T 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE T 71 " --> pdb=" O ILE T 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG T 8 " --> pdb=" O ILE T 69 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL V 48 " --> pdb=" O ILE V 35 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL V 48 " --> pdb=" O ILE V 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA V 31 " --> pdb=" O ILE V 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE V 16 " --> pdb=" O ALA V 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL V 33 " --> pdb=" O ASP V 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP V 14 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE V 6 " --> pdb=" O ILE V 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE V 71 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG V 8 " --> pdb=" O ILE V 69 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 48 through 51 removed outlier: 3.823A pdb=" N VAL W 48 " --> pdb=" O ILE W 35 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 48 through 51 removed outlier: 3.823A pdb=" N VAL W 48 " --> pdb=" O ILE W 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA W 31 " --> pdb=" O ILE W 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE W 16 " --> pdb=" O ALA W 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL W 33 " --> pdb=" O ASP W 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP W 14 " --> pdb=" O VAL W 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE W 6 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE W 71 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG W 8 " --> pdb=" O ILE W 69 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 48 through 51 removed outlier: 3.823A pdb=" N VAL X 48 " --> pdb=" O ILE X 35 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 48 through 51 removed outlier: 3.823A pdb=" N VAL X 48 " --> pdb=" O ILE X 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA X 31 " --> pdb=" O ILE X 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE X 16 " --> pdb=" O ALA X 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL X 33 " --> pdb=" O ASP X 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP X 14 " --> pdb=" O VAL X 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE X 6 " --> pdb=" O ILE X 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE X 71 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG X 8 " --> pdb=" O ILE X 69 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL Y 48 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Y' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL Y 48 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA Y 31 " --> pdb=" O ILE Y 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE Y 16 " --> pdb=" O ALA Y 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL Y 33 " --> pdb=" O ASP Y 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP Y 14 " --> pdb=" O VAL Y 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE Y 6 " --> pdb=" O ILE Y 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE Y 71 " --> pdb=" O ILE Y 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARG Y 8 " --> pdb=" O ILE Y 69 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL Z 48 " --> pdb=" O ILE Z 35 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 48 through 51 removed outlier: 3.824A pdb=" N VAL Z 48 " --> pdb=" O ILE Z 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA Z 31 " --> pdb=" O ILE Z 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE Z 16 " --> pdb=" O ALA Z 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL Z 33 " --> pdb=" O ASP Z 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP Z 14 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE Z 6 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE Z 71 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG Z 8 " --> pdb=" O ILE Z 69 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'AA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALAA 48 " --> pdb=" O ILEAA 35 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'AA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALAA 48 " --> pdb=" O ILEAA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAAA 31 " --> pdb=" O ILEAA 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILEAA 16 " --> pdb=" O ALAAA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALAA 33 " --> pdb=" O ASPAA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPAA 14 " --> pdb=" O VALAA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEAA 6 " --> pdb=" O ILEAA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEAA 71 " --> pdb=" O ILEAA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGAA 8 " --> pdb=" O ILEAA 69 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'BA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALBA 48 " --> pdb=" O ILEBA 35 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'BA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALBA 48 " --> pdb=" O ILEBA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALABA 31 " --> pdb=" O ILEBA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEBA 16 " --> pdb=" O ALABA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALBA 33 " --> pdb=" O ASPBA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPBA 14 " --> pdb=" O VALBA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEBA 6 " --> pdb=" O ILEBA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEBA 71 " --> pdb=" O ILEBA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGBA 8 " --> pdb=" O ILEBA 69 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'CA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALCA 48 " --> pdb=" O ILECA 35 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'CA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALCA 48 " --> pdb=" O ILECA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALACA 31 " --> pdb=" O ILECA 16 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILECA 16 " --> pdb=" O ALACA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALCA 33 " --> pdb=" O ASPCA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPCA 14 " --> pdb=" O VALCA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILECA 6 " --> pdb=" O ILECA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILECA 71 " --> pdb=" O ILECA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGCA 8 " --> pdb=" O ILECA 69 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'DA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALDA 48 " --> pdb=" O ILEDA 35 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'DA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALDA 48 " --> pdb=" O ILEDA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALADA 31 " --> pdb=" O ILEDA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEDA 16 " --> pdb=" O ALADA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALDA 33 " --> pdb=" O ASPDA 14 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASPDA 14 " --> pdb=" O VALDA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEDA 6 " --> pdb=" O ILEDA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEDA 71 " --> pdb=" O ILEDA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGDA 8 " --> pdb=" O ILEDA 69 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'EA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALEA 48 " --> pdb=" O ILEEA 35 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'EA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALEA 48 " --> pdb=" O ILEEA 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALAEA 31 " --> pdb=" O ILEEA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEEA 16 " --> pdb=" O ALAEA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALEA 33 " --> pdb=" O ASPEA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPEA 14 " --> pdb=" O VALEA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEEA 6 " --> pdb=" O ILEEA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEEA 71 " --> pdb=" O ILEEA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGEA 8 " --> pdb=" O ILEEA 69 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'FA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALFA 48 " --> pdb=" O ILEFA 35 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'FA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALFA 48 " --> pdb=" O ILEFA 35 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALAFA 31 " --> pdb=" O ILEFA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEFA 16 " --> pdb=" O ALAFA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALFA 33 " --> pdb=" O ASPFA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPFA 14 " --> pdb=" O VALFA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEFA 6 " --> pdb=" O ILEFA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEFA 71 " --> pdb=" O ILEFA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGFA 8 " --> pdb=" O ILEFA 69 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'GA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALGA 48 " --> pdb=" O ILEGA 35 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'GA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALGA 48 " --> pdb=" O ILEGA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAGA 31 " --> pdb=" O ILEGA 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILEGA 16 " --> pdb=" O ALAGA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALGA 33 " --> pdb=" O ASPGA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPGA 14 " --> pdb=" O VALGA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEGA 6 " --> pdb=" O ILEGA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEGA 71 " --> pdb=" O ILEGA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGGA 8 " --> pdb=" O ILEGA 69 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'HA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALHA 48 " --> pdb=" O ILEHA 35 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'HA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALHA 48 " --> pdb=" O ILEHA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAHA 31 " --> pdb=" O ILEHA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEHA 16 " --> pdb=" O ALAHA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALHA 33 " --> pdb=" O ASPHA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPHA 14 " --> pdb=" O VALHA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEHA 6 " --> pdb=" O ILEHA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEHA 71 " --> pdb=" O ILEHA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGHA 8 " --> pdb=" O ILEHA 69 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'IA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALIA 48 " --> pdb=" O ILEIA 35 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'IA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALIA 48 " --> pdb=" O ILEIA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAIA 31 " --> pdb=" O ILEIA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEIA 16 " --> pdb=" O ALAIA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALIA 33 " --> pdb=" O ASPIA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPIA 14 " --> pdb=" O VALIA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEIA 6 " --> pdb=" O ILEIA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEIA 71 " --> pdb=" O ILEIA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGIA 8 " --> pdb=" O ILEIA 69 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'JA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALJA 48 " --> pdb=" O ILEJA 35 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'JA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALJA 48 " --> pdb=" O ILEJA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAJA 31 " --> pdb=" O ILEJA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEJA 16 " --> pdb=" O ALAJA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALJA 33 " --> pdb=" O ASPJA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPJA 14 " --> pdb=" O VALJA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEJA 6 " --> pdb=" O ILEJA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEJA 71 " --> pdb=" O ILEJA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGJA 8 " --> pdb=" O ILEJA 69 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'KA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALKA 48 " --> pdb=" O ILEKA 35 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'KA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALKA 48 " --> pdb=" O ILEKA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAKA 31 " --> pdb=" O ILEKA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEKA 16 " --> pdb=" O ALAKA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALKA 33 " --> pdb=" O ASPKA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPKA 14 " --> pdb=" O VALKA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEKA 6 " --> pdb=" O ILEKA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEKA 71 " --> pdb=" O ILEKA 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARGKA 8 " --> pdb=" O ILEKA 69 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'LA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALLA 48 " --> pdb=" O ILELA 35 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'LA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALLA 48 " --> pdb=" O ILELA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALALA 31 " --> pdb=" O ILELA 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILELA 16 " --> pdb=" O ALALA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALLA 33 " --> pdb=" O ASPLA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPLA 14 " --> pdb=" O VALLA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILELA 6 " --> pdb=" O ILELA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILELA 71 " --> pdb=" O ILELA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGLA 8 " --> pdb=" O ILELA 69 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'MA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALMA 48 " --> pdb=" O ILEMA 35 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'MA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALMA 48 " --> pdb=" O ILEMA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAMA 31 " --> pdb=" O ILEMA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEMA 16 " --> pdb=" O ALAMA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALMA 33 " --> pdb=" O ASPMA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPMA 14 " --> pdb=" O VALMA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEMA 6 " --> pdb=" O ILEMA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEMA 71 " --> pdb=" O ILEMA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGMA 8 " --> pdb=" O ILEMA 69 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'NA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALNA 48 " --> pdb=" O ILENA 35 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'NA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALNA 48 " --> pdb=" O ILENA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALANA 31 " --> pdb=" O ILENA 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILENA 16 " --> pdb=" O ALANA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALNA 33 " --> pdb=" O ASPNA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPNA 14 " --> pdb=" O VALNA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILENA 6 " --> pdb=" O ILENA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILENA 71 " --> pdb=" O ILENA 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARGNA 8 " --> pdb=" O ILENA 69 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'OA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALOA 48 " --> pdb=" O ILEOA 35 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'OA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALOA 48 " --> pdb=" O ILEOA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAOA 31 " --> pdb=" O ILEOA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEOA 16 " --> pdb=" O ALAOA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALOA 33 " --> pdb=" O ASPOA 14 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASPOA 14 " --> pdb=" O VALOA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEOA 6 " --> pdb=" O ILEOA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEOA 71 " --> pdb=" O ILEOA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGOA 8 " --> pdb=" O ILEOA 69 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'PA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALPA 48 " --> pdb=" O ILEPA 35 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'PA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALPA 48 " --> pdb=" O ILEPA 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALAPA 31 " --> pdb=" O ILEPA 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILEPA 16 " --> pdb=" O ALAPA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALPA 33 " --> pdb=" O ASPPA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPPA 14 " --> pdb=" O VALPA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEPA 6 " --> pdb=" O ILEPA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEPA 71 " --> pdb=" O ILEPA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGPA 8 " --> pdb=" O ILEPA 69 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'QA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALQA 48 " --> pdb=" O ILEQA 35 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'QA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALQA 48 " --> pdb=" O ILEQA 35 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALAQA 31 " --> pdb=" O ILEQA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEQA 16 " --> pdb=" O ALAQA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALQA 33 " --> pdb=" O ASPQA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPQA 14 " --> pdb=" O VALQA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEQA 6 " --> pdb=" O ILEQA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEQA 71 " --> pdb=" O ILEQA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGQA 8 " --> pdb=" O ILEQA 69 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'RA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALRA 48 " --> pdb=" O ILERA 35 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'RA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALRA 48 " --> pdb=" O ILERA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALARA 31 " --> pdb=" O ILERA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILERA 16 " --> pdb=" O ALARA 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALRA 33 " --> pdb=" O ASPRA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPRA 14 " --> pdb=" O VALRA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILERA 6 " --> pdb=" O ILERA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILERA 71 " --> pdb=" O ILERA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGRA 8 " --> pdb=" O ILERA 69 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'SA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALSA 48 " --> pdb=" O ILESA 35 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'SA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALSA 48 " --> pdb=" O ILESA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALASA 31 " --> pdb=" O ILESA 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILESA 16 " --> pdb=" O ALASA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALSA 33 " --> pdb=" O ASPSA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPSA 14 " --> pdb=" O VALSA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILESA 6 " --> pdb=" O ILESA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILESA 71 " --> pdb=" O ILESA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGSA 8 " --> pdb=" O ILESA 69 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'TA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALTA 48 " --> pdb=" O ILETA 35 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'TA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALTA 48 " --> pdb=" O ILETA 35 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALATA 31 " --> pdb=" O ILETA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILETA 16 " --> pdb=" O ALATA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALTA 33 " --> pdb=" O ASPTA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPTA 14 " --> pdb=" O VALTA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILETA 6 " --> pdb=" O ILETA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILETA 71 " --> pdb=" O ILETA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGTA 8 " --> pdb=" O ILETA 69 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'UA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALUA 48 " --> pdb=" O ILEUA 35 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'UA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALUA 48 " --> pdb=" O ILEUA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAUA 31 " --> pdb=" O ILEUA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEUA 16 " --> pdb=" O ALAUA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALUA 33 " --> pdb=" O ASPUA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPUA 14 " --> pdb=" O VALUA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEUA 6 " --> pdb=" O ILEUA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEUA 71 " --> pdb=" O ILEUA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGUA 8 " --> pdb=" O ILEUA 69 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'VA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALVA 48 " --> pdb=" O ILEVA 35 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'VA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALVA 48 " --> pdb=" O ILEVA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAVA 31 " --> pdb=" O ILEVA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEVA 16 " --> pdb=" O ALAVA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALVA 33 " --> pdb=" O ASPVA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPVA 14 " --> pdb=" O VALVA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEVA 6 " --> pdb=" O ILEVA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEVA 71 " --> pdb=" O ILEVA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGVA 8 " --> pdb=" O ILEVA 69 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'WA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALWA 48 " --> pdb=" O ILEWA 35 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'WA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALWA 48 " --> pdb=" O ILEWA 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALAWA 31 " --> pdb=" O ILEWA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEWA 16 " --> pdb=" O ALAWA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALWA 33 " --> pdb=" O ASPWA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPWA 14 " --> pdb=" O VALWA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEWA 6 " --> pdb=" O ILEWA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEWA 71 " --> pdb=" O ILEWA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGWA 8 " --> pdb=" O ILEWA 69 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'XA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALXA 48 " --> pdb=" O ILEXA 35 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'XA' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALXA 48 " --> pdb=" O ILEXA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAXA 31 " --> pdb=" O ILEXA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEXA 16 " --> pdb=" O ALAXA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALXA 33 " --> pdb=" O ASPXA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPXA 14 " --> pdb=" O VALXA 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEXA 6 " --> pdb=" O ILEXA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEXA 71 " --> pdb=" O ILEXA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGXA 8 " --> pdb=" O ILEXA 69 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'YA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALYA 48 " --> pdb=" O ILEYA 35 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'YA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALYA 48 " --> pdb=" O ILEYA 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAYA 31 " --> pdb=" O ILEYA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEYA 16 " --> pdb=" O ALAYA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALYA 33 " --> pdb=" O ASPYA 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPYA 14 " --> pdb=" O VALYA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEYA 6 " --> pdb=" O ILEYA 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEYA 71 " --> pdb=" O ILEYA 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARGYA 8 " --> pdb=" O ILEYA 69 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'ZA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALZA 48 " --> pdb=" O ILEZA 35 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'ZA' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALZA 48 " --> pdb=" O ILEZA 35 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALAZA 31 " --> pdb=" O ILEZA 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEZA 16 " --> pdb=" O ALAZA 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALZA 33 " --> pdb=" O ASPZA 14 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASPZA 14 " --> pdb=" O VALZA 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEZA 6 " --> pdb=" O ILEZA 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEZA 71 " --> pdb=" O ILEZA 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGZA 8 " --> pdb=" O ILEZA 69 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'AB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALAB 48 " --> pdb=" O ILEAB 35 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'AB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALAB 48 " --> pdb=" O ILEAB 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAAB 31 " --> pdb=" O ILEAB 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEAB 16 " --> pdb=" O ALAAB 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALAB 33 " --> pdb=" O ASPAB 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPAB 14 " --> pdb=" O VALAB 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEAB 6 " --> pdb=" O ILEAB 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEAB 71 " --> pdb=" O ILEAB 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARGAB 8 " --> pdb=" O ILEAB 69 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'BB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALBB 48 " --> pdb=" O ILEBB 35 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'BB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALBB 48 " --> pdb=" O ILEBB 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALABB 31 " --> pdb=" O ILEBB 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEBB 16 " --> pdb=" O ALABB 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALBB 33 " --> pdb=" O ASPBB 14 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASPBB 14 " --> pdb=" O VALBB 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEBB 6 " --> pdb=" O ILEBB 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEBB 71 " --> pdb=" O ILEBB 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGBB 8 " --> pdb=" O ILEBB 69 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'CB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALCB 48 " --> pdb=" O ILECB 35 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'CB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALCB 48 " --> pdb=" O ILECB 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALACB 31 " --> pdb=" O ILECB 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILECB 16 " --> pdb=" O ALACB 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALCB 33 " --> pdb=" O ASPCB 14 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASPCB 14 " --> pdb=" O VALCB 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILECB 6 " --> pdb=" O ILECB 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILECB 71 " --> pdb=" O ILECB 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGCB 8 " --> pdb=" O ILECB 69 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'DB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALDB 48 " --> pdb=" O ILEDB 35 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'DB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALDB 48 " --> pdb=" O ILEDB 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALADB 31 " --> pdb=" O ILEDB 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEDB 16 " --> pdb=" O ALADB 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALDB 33 " --> pdb=" O ASPDB 14 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASPDB 14 " --> pdb=" O VALDB 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEDB 6 " --> pdb=" O ILEDB 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEDB 71 " --> pdb=" O ILEDB 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARGDB 8 " --> pdb=" O ILEDB 69 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'EB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALEB 48 " --> pdb=" O ILEEB 35 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'EB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALEB 48 " --> pdb=" O ILEEB 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAEB 31 " --> pdb=" O ILEEB 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEEB 16 " --> pdb=" O ALAEB 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALEB 33 " --> pdb=" O ASPEB 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPEB 14 " --> pdb=" O VALEB 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEEB 6 " --> pdb=" O ILEEB 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEEB 71 " --> pdb=" O ILEEB 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGEB 8 " --> pdb=" O ILEEB 69 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'FB' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALFB 48 " --> pdb=" O ILEFB 35 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'FB' and resid 48 through 51 removed outlier: 3.825A pdb=" N VALFB 48 " --> pdb=" O ILEFB 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAFB 31 " --> pdb=" O ILEFB 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEFB 16 " --> pdb=" O ALAFB 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALFB 33 " --> pdb=" O ASPFB 14 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASPFB 14 " --> pdb=" O VALFB 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILEFB 6 " --> pdb=" O ILEFB 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEFB 71 " --> pdb=" O ILEFB 6 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARGFB 8 " --> pdb=" O ILEFB 69 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'GB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALGB 48 " --> pdb=" O ILEGB 35 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'GB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALGB 48 " --> pdb=" O ILEGB 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAGB 31 " --> pdb=" O ILEGB 16 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILEGB 16 " --> pdb=" O ALAGB 31 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VALGB 33 " --> pdb=" O ASPGB 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPGB 14 " --> pdb=" O VALGB 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEGB 6 " --> pdb=" O ILEGB 71 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILEGB 71 " --> pdb=" O ILEGB 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGGB 8 " --> pdb=" O ILEGB 69 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'HB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALHB 48 " --> pdb=" O ILEHB 35 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'HB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALHB 48 " --> pdb=" O ILEHB 35 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALAHB 31 " --> pdb=" O ILEHB 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEHB 16 " --> pdb=" O ALAHB 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALHB 33 " --> pdb=" O ASPHB 14 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASPHB 14 " --> pdb=" O VALHB 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEHB 6 " --> pdb=" O ILEHB 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEHB 71 " --> pdb=" O ILEHB 6 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARGHB 8 " --> pdb=" O ILEHB 69 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'IB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALIB 48 " --> pdb=" O ILEIB 35 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'IB' and resid 48 through 51 removed outlier: 3.824A pdb=" N VALIB 48 " --> pdb=" O ILEIB 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALAIB 31 " --> pdb=" O ILEIB 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILEIB 16 " --> pdb=" O ALAIB 31 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VALIB 33 " --> pdb=" O ASPIB 14 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASPIB 14 " --> pdb=" O VALIB 33 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILEIB 6 " --> pdb=" O ILEIB 71 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILEIB 71 " --> pdb=" O ILEIB 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ARGIB 8 " --> pdb=" O ILEIB 69 " (cutoff:3.500A) 3840 hydrogen bonds defined for protein. 11340 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: 26.66 Time building geometry restraints manager: 13.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 20280 1.34 - 1.46: 6765 1.46 - 1.57: 33255 1.57 - 1.69: 0 1.69 - 1.80: 360 Bond restraints: 60660 Sorted by residual: bond pdb=" C ARG M 109 " pdb=" O ARG M 109 " ideal model delta sigma weight residual 1.237 1.242 -0.006 1.17e-02 7.31e+03 2.40e-01 bond pdb=" C ARGCB 109 " pdb=" O ARGCB 109 " ideal model delta sigma weight residual 1.237 1.242 -0.006 1.17e-02 7.31e+03 2.39e-01 bond pdb=" C ARG Z 109 " pdb=" O ARG Z 109 " ideal model delta sigma weight residual 1.237 1.242 -0.006 1.17e-02 7.31e+03 2.33e-01 bond pdb=" C ARGFB 109 " pdb=" O ARGFB 109 " ideal model delta sigma weight residual 1.237 1.242 -0.006 1.17e-02 7.31e+03 2.31e-01 bond pdb=" C ARG F 109 " pdb=" O ARG F 109 " ideal model delta sigma weight residual 1.237 1.242 -0.006 1.17e-02 7.31e+03 2.30e-01 ... (remaining 60655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 78378 0.88 - 1.76: 2299 1.76 - 2.64: 563 2.64 - 3.52: 240 3.52 - 4.39: 60 Bond angle restraints: 81540 Sorted by residual: angle pdb=" C THR Q 86 " pdb=" N ARG Q 87 " pdb=" CA ARG Q 87 " ideal model delta sigma weight residual 121.52 118.05 3.47 1.84e+00 2.95e-01 3.55e+00 angle pdb=" C THR E 86 " pdb=" N ARG E 87 " pdb=" CA ARG E 87 " ideal model delta sigma weight residual 121.52 118.06 3.46 1.84e+00 2.95e-01 3.53e+00 angle pdb=" C THRXA 86 " pdb=" N ARGXA 87 " pdb=" CA ARGXA 87 " ideal model delta sigma weight residual 121.52 118.07 3.45 1.84e+00 2.95e-01 3.52e+00 angle pdb=" C THR V 86 " pdb=" N ARG V 87 " pdb=" CA ARG V 87 " ideal model delta sigma weight residual 121.52 118.07 3.45 1.84e+00 2.95e-01 3.51e+00 angle pdb=" C THRZA 86 " pdb=" N ARGZA 87 " pdb=" CA ARGZA 87 " ideal model delta sigma weight residual 121.52 118.07 3.45 1.84e+00 2.95e-01 3.51e+00 ... (remaining 81535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 34860 17.86 - 35.71: 3284 35.71 - 53.57: 496 53.57 - 71.43: 60 71.43 - 89.28: 180 Dihedral angle restraints: 38880 sinusoidal: 17100 harmonic: 21780 Sorted by residual: dihedral pdb=" CG ARGBA 8 " pdb=" CD ARGBA 8 " pdb=" NE ARGBA 8 " pdb=" CZ ARGBA 8 " ideal model delta sinusoidal sigma weight residual -90.00 -134.84 44.84 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARGPA 8 " pdb=" CD ARGPA 8 " pdb=" NE ARGPA 8 " pdb=" CZ ARGPA 8 " ideal model delta sinusoidal sigma weight residual -90.00 -134.83 44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARGZA 8 " pdb=" CD ARGZA 8 " pdb=" NE ARGZA 8 " pdb=" CZ ARGZA 8 " ideal model delta sinusoidal sigma weight residual -90.00 -134.83 44.83 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 38877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 6433 0.028 - 0.056: 1694 0.056 - 0.084: 807 0.084 - 0.112: 489 0.112 - 0.139: 357 Chirality restraints: 9780 Sorted by residual: chirality pdb=" CA ILEUA 71 " pdb=" N ILEUA 71 " pdb=" C ILEUA 71 " pdb=" CB ILEUA 71 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE W 71 " pdb=" N ILE W 71 " pdb=" C ILE W 71 " pdb=" CB ILE W 71 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE X 71 " pdb=" N ILE X 71 " pdb=" C ILE X 71 " pdb=" CB ILE X 71 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 9777 not shown) Planarity restraints: 10380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 50 " -0.010 5.00e-02 4.00e+02 1.54e-02 3.80e-01 pdb=" N PRO C 51 " 0.027 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER O 50 " -0.010 5.00e-02 4.00e+02 1.54e-02 3.78e-01 pdb=" N PRO O 51 " 0.027 5.00e-02 4.00e+02 pdb=" CA PRO O 51 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO O 51 " -0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 50 " -0.010 5.00e-02 4.00e+02 1.53e-02 3.75e-01 pdb=" N PRO K 51 " 0.026 5.00e-02 4.00e+02 pdb=" CA PRO K 51 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO K 51 " -0.009 5.00e-02 4.00e+02 ... (remaining 10377 not shown) Histogram of nonbonded interaction distances: 2.50 - 3.01: 31885 3.01 - 3.53: 69331 3.53 - 4.04: 87607 4.04 - 4.55: 120273 4.55 - 5.06: 184672 Nonbonded interactions: 493768 Sorted by model distance: nonbonded pdb=" O SERCB 117 " pdb=" OG SERCB 117 " model vdw 2.503 3.040 nonbonded pdb=" O SER Y 117 " pdb=" OG SER Y 117 " model vdw 2.503 3.040 nonbonded pdb=" O SER L 117 " pdb=" OG SER L 117 " model vdw 2.503 3.040 nonbonded pdb=" O SERBB 117 " pdb=" OG SERBB 117 " model vdw 2.503 3.040 nonbonded pdb=" O SER T 117 " pdb=" OG SER T 117 " model vdw 2.503 3.040 ... (remaining 493763 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 'A' and resid 2 through 132) selection = (chain 'AA' and resid 2 through 132) selection = (chain 'AB' and resid 2 through 132) selection = (chain 'B' and resid 2 through 132) selection = (chain 'BA' and resid 2 through 132) selection = (chain 'BB' and resid 2 through 132) selection = (chain 'C' and resid 2 through 132) selection = (chain 'CA' and resid 2 through 132) selection = (chain 'CB' and resid 2 through 132) selection = (chain 'D' and resid 2 through 132) selection = (chain 'DA' and resid 2 through 132) selection = (chain 'DB' and resid 2 through 132) selection = (chain 'E' and resid 2 through 132) selection = (chain 'EA' and resid 2 through 132) selection = (chain 'EB' and resid 2 through 132) selection = (chain 'F' and resid 2 through 132) selection = (chain 'FA' and resid 2 through 132) selection = (chain 'FB' and resid 2 through 132) selection = (chain 'G' and resid 2 through 132) selection = (chain 'GA' and resid 2 through 132) selection = (chain 'GB' and resid 2 through 132) selection = (chain 'H' and resid 2 through 132) selection = chain 'HA' selection = (chain 'HB' and resid 2 through 132) selection = (chain 'I' and resid 2 through 132) selection = (chain 'IA' and resid 2 through 132) selection = (chain 'IB' and resid 2 through 132) selection = chain 'J' selection = (chain 'JA' and resid 2 through 132) selection = (chain 'K' and resid 2 through 132) selection = (chain 'KA' and resid 2 through 132) selection = (chain 'L' and resid 2 through 132) selection = (chain 'LA' and resid 2 through 132) selection = (chain 'M' and resid 2 through 132) selection = (chain 'MA' and resid 2 through 132) selection = (chain 'N' and resid 2 through 132) selection = chain 'NA' selection = (chain 'O' and resid 2 through 132) selection = (chain 'OA' and resid 2 through 132) selection = chain 'P' selection = chain 'PA' selection = chain 'Q' selection = (chain 'QA' and resid 2 through 132) selection = chain 'R' selection = chain 'RA' selection = (chain 'S' and resid 2 through 132) selection = (chain 'SA' and resid 2 through 132) selection = chain 'T' selection = (chain 'TA' and resid 2 through 132) selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = (chain 'Y' and resid 2 through 132) selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.780 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: 0.060 Extract box with map and model: 2.130 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 107.490 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.770 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 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 : 0.002 0.015 60660 Z= 0.156 Angle : 0.429 4.394 81540 Z= 0.222 Chirality : 0.043 0.139 9780 Planarity : 0.002 0.015 10380 Dihedral : 15.165 89.284 24480 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.10), residues: 7140 helix: 4.13 (0.07), residues: 3240 sheet: 0.67 (0.16), residues: 1320 loop : -1.59 (0.10), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 52 HIS 0.001 0.000 HISZA 85 PHE 0.002 0.001 PHE B 32 TYR 0.007 0.001 TYR J 82 ARG 0.001 0.000 ARG Q 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1759 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1759 time to evaluate : 5.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8509 (tttt) REVERT: B 108 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7664 (tm-30) REVERT: C 102 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8591 (ttmm) REVERT: C 108 GLN cc_start: 0.8406 (tm-30) cc_final: 0.7901 (tm-30) REVERT: E 108 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7640 (tm-30) REVERT: F 102 LYS cc_start: 0.8770 (ttpp) cc_final: 0.8496 (tttt) REVERT: F 108 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7756 (tm-30) REVERT: G 108 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7682 (tm-30) REVERT: G 109 ARG cc_start: 0.8346 (tmm-80) cc_final: 0.8106 (tmm-80) REVERT: H 94 VAL cc_start: 0.8037 (t) cc_final: 0.7756 (t) REVERT: H 102 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8597 (ttmm) REVERT: H 108 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8041 (tm-30) REVERT: J 108 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7700 (tm-30) REVERT: K 102 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8484 (tttt) REVERT: L 65 ASP cc_start: 0.7997 (p0) cc_final: 0.7724 (p0) REVERT: M 102 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8600 (ttmm) REVERT: M 108 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7900 (tm-30) REVERT: N 108 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7841 (tm-30) REVERT: O 108 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7576 (tm-30) REVERT: P 102 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8534 (tttt) REVERT: P 108 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7761 (tm-30) REVERT: Q 108 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7699 (tm-30) REVERT: R 108 GLN cc_start: 0.8385 (tm-30) cc_final: 0.7927 (tm-30) REVERT: T 108 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7903 (tm-30) REVERT: V 102 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8545 (tttt) REVERT: V 108 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7635 (tm-30) REVERT: W 65 ASP cc_start: 0.7928 (p0) cc_final: 0.7679 (p0) REVERT: W 108 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7650 (tm-30) REVERT: W 109 ARG cc_start: 0.8374 (tmm-80) cc_final: 0.8139 (tmm-80) REVERT: Y 108 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7819 (tm-30) REVERT: Z 108 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7629 (tm-30) REVERT: AA 102 LYS cc_start: 0.8810 (ttpp) cc_final: 0.8494 (tttt) REVERT: AA 108 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7690 (tm-30) REVERT: CA 102 LYS cc_start: 0.8823 (ttpp) cc_final: 0.8575 (ttmm) REVERT: CA 108 GLN cc_start: 0.8410 (tm-30) cc_final: 0.7923 (tm-30) REVERT: FA 102 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8531 (tttt) REVERT: FA 108 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7689 (tm-30) REVERT: GA 65 ASP cc_start: 0.7980 (p0) cc_final: 0.7707 (p0) REVERT: GA 108 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7669 (tm-30) REVERT: HA 108 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8245 (tm-30) REVERT: JA 108 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7706 (tm-30) REVERT: KA 102 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8496 (tttt) REVERT: LA 65 ASP cc_start: 0.7951 (p0) cc_final: 0.7672 (p0) REVERT: MA 110 MET cc_start: 0.8466 (tmm) cc_final: 0.7934 (ttm) REVERT: OA 108 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7991 (tm-30) REVERT: PA 102 LYS cc_start: 0.8808 (ttpp) cc_final: 0.8552 (tttt) REVERT: PA 108 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7716 (tm-30) REVERT: QA 108 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7679 (tm-30) REVERT: RA 102 LYS cc_start: 0.8832 (ttpp) cc_final: 0.8590 (ttmm) REVERT: TA 108 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7683 (tm-30) REVERT: UA 102 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8560 (tttt) REVERT: VA 108 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7655 (tm-30) REVERT: WA 102 LYS cc_start: 0.8819 (ttpp) cc_final: 0.8603 (ttmm) REVERT: WA 110 MET cc_start: 0.8488 (tmm) cc_final: 0.7856 (ttm) REVERT: YA 102 LYS cc_start: 0.8886 (ttpp) cc_final: 0.8600 (tttt) REVERT: YA 108 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7714 (tm-30) REVERT: ZA 102 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8508 (tttt) REVERT: ZA 108 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7752 (tm-30) REVERT: AB 65 ASP cc_start: 0.7937 (p0) cc_final: 0.7613 (p0) REVERT: AB 108 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7649 (tm-30) REVERT: CB 108 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7744 (tm-30) REVERT: DB 102 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8702 (tttt) REVERT: EB 102 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8557 (tttt) REVERT: EB 108 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7631 (tm-30) REVERT: FB 65 ASP cc_start: 0.7965 (p0) cc_final: 0.7680 (p0) REVERT: GB 102 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8604 (ttmm) REVERT: GB 108 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8034 (tm-30) REVERT: HB 110 MET cc_start: 0.8514 (tmm) cc_final: 0.7941 (ttm) REVERT: IB 108 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7615 (tm-30) outliers start: 0 outliers final: 0 residues processed: 1759 average time/residue: 0.6343 time to fit residues: 1788.0813 Evaluate side-chains 1125 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1125 time to evaluate : 5.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 4.9990 chunk 545 optimal weight: 7.9990 chunk 302 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 368 optimal weight: 10.0000 chunk 291 optimal weight: 6.9990 chunk 564 optimal weight: 7.9990 chunk 218 optimal weight: 8.9990 chunk 343 optimal weight: 6.9990 chunk 420 optimal weight: 10.0000 chunk 653 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS B 85 HIS C 85 HIS D 114 GLN E 85 HIS F 85 HIS F 114 GLN G 85 HIS G 132 GLN H 85 HIS H 132 GLN I 85 HIS J 85 HIS J 114 GLN K 85 HIS L 85 HIS L 132 GLN M 85 HIS N 85 HIS N 127 GLN O 85 HIS P 85 HIS P 114 GLN Q 85 HIS R 85 HIS S 85 HIS T 85 HIS V 85 HIS W 85 HIS W 132 GLN X 85 HIS Z 85 HIS AA 85 HIS AA 114 GLN BA 85 HIS BA 114 GLN CA 85 HIS DA 114 GLN EA 85 HIS EA 114 GLN FA 85 HIS FA 114 GLN GA 85 HIS HA 85 HIS IA 85 HIS JA 85 HIS KA 85 HIS LA 85 HIS LA 132 GLN MA 85 HIS MA 132 GLN NA 85 HIS NA 127 GLN OA 85 HIS PA 85 HIS QA 85 HIS RA 85 HIS SA 85 HIS TA 85 HIS TA 114 GLN UA 85 HIS UA 114 GLN VA 85 HIS VA 114 GLN WA 85 HIS WA 132 GLN YA 85 HIS YA 114 GLN ZA 85 HIS ZA 114 GLN AB 85 HIS BB 85 HIS DB 85 HIS EB 85 HIS EB 114 GLN FB 85 HIS GB 85 HIS HB 85 HIS IB 85 HIS Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 60660 Z= 0.478 Angle : 0.677 6.484 81540 Z= 0.358 Chirality : 0.048 0.157 9780 Planarity : 0.003 0.037 10380 Dihedral : 3.935 14.253 7740 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.26 % Allowed : 9.72 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.10), residues: 7140 helix: 2.83 (0.08), residues: 3300 sheet: 0.24 (0.15), residues: 1320 loop : -1.40 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 52 HIS 0.004 0.002 HISGA 85 PHE 0.011 0.003 PHE D 32 TYR 0.012 0.002 TYRSA 82 ARG 0.005 0.001 ARGOA 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 1057 time to evaluate : 5.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7993 (ttmt) REVERT: E 108 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7648 (tm-30) REVERT: G 14 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: G 65 ASP cc_start: 0.8000 (p0) cc_final: 0.7764 (p0) REVERT: H 96 GLU cc_start: 0.7233 (tt0) cc_final: 0.6765 (tt0) REVERT: K 57 ASP cc_start: 0.7944 (m-30) cc_final: 0.7694 (m-30) REVERT: L 14 ASP cc_start: 0.8317 (OUTLIER) cc_final: 0.7830 (m-30) REVERT: L 65 ASP cc_start: 0.7961 (p0) cc_final: 0.7715 (p0) REVERT: N 108 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7872 (tm-30) REVERT: O 108 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7633 (tm-30) REVERT: P 57 ASP cc_start: 0.7930 (m-30) cc_final: 0.7728 (m-30) REVERT: Q 14 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: Q 108 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7649 (tm-30) REVERT: T 108 GLN cc_start: 0.8428 (tm-30) cc_final: 0.7851 (tm-30) REVERT: W 14 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: W 65 ASP cc_start: 0.7977 (p0) cc_final: 0.7733 (p0) REVERT: W 96 GLU cc_start: 0.7179 (tt0) cc_final: 0.6968 (tt0) REVERT: X 108 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7911 (tm-30) REVERT: Y 108 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7899 (tm-30) REVERT: Z 108 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7657 (tm-30) REVERT: CA 96 GLU cc_start: 0.7233 (tt0) cc_final: 0.6811 (tt0) REVERT: GA 65 ASP cc_start: 0.8004 (p0) cc_final: 0.7780 (p0) REVERT: HA 108 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8145 (tm-30) REVERT: LA 14 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: LA 65 ASP cc_start: 0.7921 (p0) cc_final: 0.7699 (p0) REVERT: LA 96 GLU cc_start: 0.7199 (tt0) cc_final: 0.6996 (tt0) REVERT: MA 96 GLU cc_start: 0.7199 (tt0) cc_final: 0.6730 (tt0) REVERT: MA 110 MET cc_start: 0.8592 (tmm) cc_final: 0.7925 (ttm) REVERT: NA 96 GLU cc_start: 0.7075 (tt0) cc_final: 0.6866 (tt0) REVERT: NA 108 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7870 (tm-30) REVERT: OA 23 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7658 (tp-100) REVERT: OA 108 GLN cc_start: 0.8340 (tm-30) cc_final: 0.7708 (tm-30) REVERT: QA 14 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: QA 65 ASP cc_start: 0.7961 (p0) cc_final: 0.7751 (p0) REVERT: RA 96 GLU cc_start: 0.7212 (tt0) cc_final: 0.6863 (tt0) REVERT: RA 102 LYS cc_start: 0.8947 (ttpp) cc_final: 0.8605 (ttmm) REVERT: TA 108 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7640 (tm-30) REVERT: UA 57 ASP cc_start: 0.7904 (m-30) cc_final: 0.7695 (m-30) REVERT: WA 96 GLU cc_start: 0.7211 (tt0) cc_final: 0.6902 (tt0) REVERT: YA 108 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7659 (tm-30) REVERT: AB 65 ASP cc_start: 0.7922 (p0) cc_final: 0.7719 (p0) REVERT: AB 108 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7622 (tm-30) REVERT: CB 108 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7799 (tm-30) REVERT: DB 108 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7691 (tm-30) REVERT: FB 14 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: FB 65 ASP cc_start: 0.7936 (p0) cc_final: 0.7697 (p0) REVERT: FB 96 GLU cc_start: 0.7213 (tt0) cc_final: 0.7009 (tt0) REVERT: GB 96 GLU cc_start: 0.7201 (tt0) cc_final: 0.6767 (tt0) REVERT: HB 110 MET cc_start: 0.8682 (tmm) cc_final: 0.7968 (ttm) outliers start: 160 outliers final: 129 residues processed: 1170 average time/residue: 0.6241 time to fit residues: 1182.7571 Evaluate side-chains 1047 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 911 time to evaluate : 5.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASP Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 127 GLN Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 70 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 96 GLU Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain S residue 127 GLN Chi-restraints excluded: chain T residue 14 ASP Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 94 VAL Chi-restraints excluded: chain V residue 14 ASP Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain X residue 18 ASN Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 123 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain AA residue 14 ASP Chi-restraints excluded: chain AA residue 70 THR Chi-restraints excluded: chain AA residue 123 LEU Chi-restraints excluded: chain AA residue 127 GLN Chi-restraints excluded: chain BA residue 70 THR Chi-restraints excluded: chain BA residue 123 LEU Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain DA residue 70 THR Chi-restraints excluded: chain DA residue 94 VAL Chi-restraints excluded: chain DA residue 96 GLU Chi-restraints excluded: chain DA residue 123 LEU Chi-restraints excluded: chain DA residue 127 GLN Chi-restraints excluded: chain EA residue 70 THR Chi-restraints excluded: chain EA residue 94 VAL Chi-restraints excluded: chain FA residue 14 ASP Chi-restraints excluded: chain FA residue 70 THR Chi-restraints excluded: chain FA residue 123 LEU Chi-restraints excluded: chain FA residue 127 GLN Chi-restraints excluded: chain GA residue 70 THR Chi-restraints excluded: chain GA residue 123 LEU Chi-restraints excluded: chain GA residue 127 GLN Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 94 VAL Chi-restraints excluded: chain IA residue 123 LEU Chi-restraints excluded: chain JA residue 70 THR Chi-restraints excluded: chain KA residue 14 ASP Chi-restraints excluded: chain KA residue 70 THR Chi-restraints excluded: chain KA residue 123 LEU Chi-restraints excluded: chain LA residue 14 ASP Chi-restraints excluded: chain LA residue 70 THR Chi-restraints excluded: chain LA residue 123 LEU Chi-restraints excluded: chain MA residue 70 THR Chi-restraints excluded: chain NA residue 70 THR Chi-restraints excluded: chain NA residue 123 LEU Chi-restraints excluded: chain OA residue 14 ASP Chi-restraints excluded: chain OA residue 70 THR Chi-restraints excluded: chain OA residue 94 VAL Chi-restraints excluded: chain PA residue 14 ASP Chi-restraints excluded: chain PA residue 70 THR Chi-restraints excluded: chain PA residue 123 LEU Chi-restraints excluded: chain PA residue 127 GLN Chi-restraints excluded: chain QA residue 14 ASP Chi-restraints excluded: chain QA residue 70 THR Chi-restraints excluded: chain QA residue 123 LEU Chi-restraints excluded: chain RA residue 70 THR Chi-restraints excluded: chain SA residue 70 THR Chi-restraints excluded: chain SA residue 127 GLN Chi-restraints excluded: chain TA residue 14 ASP Chi-restraints excluded: chain TA residue 70 THR Chi-restraints excluded: chain TA residue 94 VAL Chi-restraints excluded: chain UA residue 14 ASP Chi-restraints excluded: chain UA residue 70 THR Chi-restraints excluded: chain UA residue 123 LEU Chi-restraints excluded: chain VA residue 70 THR Chi-restraints excluded: chain VA residue 123 LEU Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain XA residue 70 THR Chi-restraints excluded: chain XA residue 94 VAL Chi-restraints excluded: chain XA residue 127 GLN Chi-restraints excluded: chain YA residue 70 THR Chi-restraints excluded: chain YA residue 94 VAL Chi-restraints excluded: chain ZA residue 14 ASP Chi-restraints excluded: chain ZA residue 70 THR Chi-restraints excluded: chain ZA residue 123 LEU Chi-restraints excluded: chain ZA residue 127 GLN Chi-restraints excluded: chain AB residue 14 ASP Chi-restraints excluded: chain AB residue 70 THR Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 123 LEU Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain CB residue 123 LEU Chi-restraints excluded: chain DB residue 70 THR Chi-restraints excluded: chain EB residue 14 ASP Chi-restraints excluded: chain EB residue 70 THR Chi-restraints excluded: chain EB residue 123 LEU Chi-restraints excluded: chain FB residue 14 ASP Chi-restraints excluded: chain FB residue 70 THR Chi-restraints excluded: chain FB residue 123 LEU Chi-restraints excluded: chain GB residue 70 THR Chi-restraints excluded: chain HB residue 70 THR Chi-restraints excluded: chain HB residue 123 LEU Chi-restraints excluded: chain IB residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 544 optimal weight: 7.9990 chunk 445 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 655 optimal weight: 2.9990 chunk 707 optimal weight: 9.9990 chunk 583 optimal weight: 1.9990 chunk 649 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 525 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 GLN B 132 GLN C 132 GLN D 114 GLN F 132 GLN G 132 GLN H 132 GLN I 114 GLN K 114 GLN L 132 GLN M 132 GLN N 114 GLN P 132 GLN Q 132 GLN R 132 GLN V 132 GLN W 132 GLN Y 114 GLN BA 132 GLN CA 132 GLN GA 132 GLN HA 132 GLN LA 132 GLN MA 132 GLN NA 114 GLN PA 132 GLN QA 132 GLN VA 132 GLN WA 132 GLN EB 114 GLN EB 132 GLN FB 132 GLN GB 132 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 60660 Z= 0.254 Angle : 0.506 4.820 81540 Z= 0.264 Chirality : 0.044 0.167 9780 Planarity : 0.003 0.028 10380 Dihedral : 3.605 13.394 7740 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.03 % Allowed : 14.96 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.10), residues: 7140 helix: 3.50 (0.07), residues: 3300 sheet: -0.43 (0.15), residues: 1020 loop : -0.79 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRPCA 52 HIS 0.002 0.001 HISDA 85 PHE 0.007 0.002 PHEZA 32 TYR 0.007 0.001 TYR T 82 ARG 0.007 0.001 ARGAB 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 1015 time to evaluate : 6.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 96 GLU cc_start: 0.7245 (tt0) cc_final: 0.6821 (tt0) REVERT: C 108 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7790 (tm-30) REVERT: E 108 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7899 (tm-30) REVERT: G 108 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7644 (tm-30) REVERT: H 60 GLU cc_start: 0.8021 (pm20) cc_final: 0.7779 (pm20) REVERT: H 108 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7805 (tm-30) REVERT: L 14 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7922 (m-30) REVERT: L 108 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7606 (tm-30) REVERT: M 60 GLU cc_start: 0.7941 (pm20) cc_final: 0.7735 (pm20) REVERT: M 96 GLU cc_start: 0.7226 (tt0) cc_final: 0.6798 (tt0) REVERT: M 108 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7789 (tm-30) REVERT: N 108 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7821 (tm-30) REVERT: O 108 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7902 (tm-30) REVERT: P 108 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7685 (tm-30) REVERT: Q 14 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: Q 108 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7567 (tm-30) REVERT: R 96 GLU cc_start: 0.7066 (tt0) cc_final: 0.6770 (tt0) REVERT: T 108 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7706 (tm-30) REVERT: V 108 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7900 (tm-30) REVERT: W 108 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7634 (tm-30) REVERT: X 60 GLU cc_start: 0.8049 (pm20) cc_final: 0.7759 (pm20) REVERT: Y 108 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7736 (tm-30) REVERT: Z 108 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7546 (tm-30) REVERT: AA 108 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7922 (tm-30) REVERT: BA 108 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7535 (tm-30) REVERT: CA 60 GLU cc_start: 0.7932 (pm20) cc_final: 0.7716 (pm20) REVERT: FA 108 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7922 (tm-30) REVERT: GA 108 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7676 (tm-30) REVERT: HA 108 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7727 (tm-30) REVERT: JA 108 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7893 (tm-30) REVERT: LA 108 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7586 (tm-30) REVERT: MA 60 GLU cc_start: 0.8038 (pm20) cc_final: 0.7804 (pm20) REVERT: MA 96 GLU cc_start: 0.7143 (tt0) cc_final: 0.6670 (tt0) REVERT: MA 110 MET cc_start: 0.8521 (tmm) cc_final: 0.7884 (ttm) REVERT: NA 96 GLU cc_start: 0.7052 (tt0) cc_final: 0.6850 (tt0) REVERT: NA 108 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7783 (tm-30) REVERT: OA 108 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7586 (tm-30) REVERT: PA 108 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7909 (tm-30) REVERT: QA 108 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7635 (tm-30) REVERT: TA 108 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7910 (tm-30) REVERT: UA 57 ASP cc_start: 0.7945 (m-30) cc_final: 0.7735 (m-30) REVERT: VA 108 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7513 (tm-30) REVERT: WA 96 GLU cc_start: 0.7189 (tt0) cc_final: 0.6732 (tt0) REVERT: WA 110 MET cc_start: 0.8574 (tmm) cc_final: 0.7915 (ttm) REVERT: YA 108 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7629 (tm-30) REVERT: ZA 108 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7924 (tm-30) REVERT: AB 14 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: AB 108 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7615 (tm-30) REVERT: CB 108 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7723 (tm-30) REVERT: DB 108 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7590 (tm-30) REVERT: EB 108 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7913 (tm-30) REVERT: FB 108 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7602 (tm-30) REVERT: GB 96 GLU cc_start: 0.7140 (tt0) cc_final: 0.6713 (tt0) REVERT: HB 108 GLN cc_start: 0.8314 (tm-30) cc_final: 0.7771 (tm-30) REVERT: HB 110 MET cc_start: 0.8603 (tmm) cc_final: 0.7984 (ttm) REVERT: IB 108 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7544 (tm-30) outliers start: 73 outliers final: 56 residues processed: 1079 average time/residue: 0.6633 time to fit residues: 1176.7987 Evaluate side-chains 989 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 930 time to evaluate : 5.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain L residue 14 ASP Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain P residue 14 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain T residue 94 VAL Chi-restraints excluded: chain V residue 70 THR Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain W residue 127 GLN Chi-restraints excluded: chain X residue 18 ASN Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain Y residue 123 LEU Chi-restraints excluded: chain AA residue 70 THR Chi-restraints excluded: chain AA residue 123 LEU Chi-restraints excluded: chain BA residue 123 LEU Chi-restraints excluded: chain DA residue 94 VAL Chi-restraints excluded: chain DA residue 123 LEU Chi-restraints excluded: chain EA residue 94 VAL Chi-restraints excluded: chain FA residue 70 THR Chi-restraints excluded: chain FA residue 123 LEU Chi-restraints excluded: chain GA residue 123 LEU Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 94 VAL Chi-restraints excluded: chain KA residue 70 THR Chi-restraints excluded: chain LA residue 123 LEU Chi-restraints excluded: chain LA residue 127 GLN Chi-restraints excluded: chain MA residue 70 THR Chi-restraints excluded: chain NA residue 123 LEU Chi-restraints excluded: chain OA residue 94 VAL Chi-restraints excluded: chain PA residue 70 THR Chi-restraints excluded: chain QA residue 123 LEU Chi-restraints excluded: chain RA residue 70 THR Chi-restraints excluded: chain SA residue 123 LEU Chi-restraints excluded: chain SA residue 127 GLN Chi-restraints excluded: chain TA residue 94 VAL Chi-restraints excluded: chain UA residue 70 THR Chi-restraints excluded: chain VA residue 123 LEU Chi-restraints excluded: chain XA residue 94 VAL Chi-restraints excluded: chain XA residue 123 LEU Chi-restraints excluded: chain YA residue 94 VAL Chi-restraints excluded: chain ZA residue 70 THR Chi-restraints excluded: chain ZA residue 123 LEU Chi-restraints excluded: chain AB residue 14 ASP Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 123 LEU Chi-restraints excluded: chain EB residue 70 THR Chi-restraints excluded: chain EB residue 123 LEU Chi-restraints excluded: chain FB residue 123 LEU Chi-restraints excluded: chain HB residue 123 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 10.0000 chunk 492 optimal weight: 4.9990 chunk 339 optimal weight: 0.0870 chunk 72 optimal weight: 0.6980 chunk 312 optimal weight: 5.9990 chunk 439 optimal weight: 5.9990 chunk 657 optimal weight: 10.0000 chunk 695 optimal weight: 20.0000 chunk 343 optimal weight: 6.9990 chunk 623 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 overall best weight: 2.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN C 132 GLN E 114 GLN F 114 GLN F 132 GLN G 132 GLN J 114 GLN L 132 GLN M 132 GLN O 114 GLN P 132 GLN Q 132 GLN V 132 GLN W 132 GLN Z 114 GLN BA 132 GLN CA 132 GLN GA 132 GLN LA 132 GLN PA 132 GLN QA 132 GLN TA 114 GLN VA 132 GLN WA 132 GLN YA 114 GLN EB 132 GLN FB 132 GLN GB 132 GLN IB 114 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 60660 Z= 0.209 Angle : 0.475 4.868 81540 Z= 0.246 Chirality : 0.044 0.169 9780 Planarity : 0.003 0.034 10380 Dihedral : 3.445 12.269 7740 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.50 % Allowed : 17.71 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.10), residues: 7140 helix: 3.83 (0.07), residues: 3300 sheet: -0.49 (0.15), residues: 1020 loop : -0.77 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRPMA 52 HIS 0.002 0.001 HIS Y 85 PHE 0.005 0.001 PHE Q 32 TYR 0.006 0.001 TYRAB 82 ARG 0.008 0.000 ARGGA 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 993 time to evaluate : 5.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7656 (tm-30) REVERT: C 108 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7817 (tm-30) REVERT: E 108 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7469 (tm-30) REVERT: F 108 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7675 (tm-30) REVERT: F 114 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.6893 (tt0) REVERT: G 108 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7651 (tm-30) REVERT: H 108 GLN cc_start: 0.8320 (tm-30) cc_final: 0.7791 (tm-30) REVERT: J 108 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7601 (tm-30) REVERT: L 108 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7613 (tm-30) REVERT: L 109 ARG cc_start: 0.8469 (tmm-80) cc_final: 0.8144 (tmm-80) REVERT: M 108 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7784 (tm-30) REVERT: N 99 ARG cc_start: 0.8481 (tmm-80) cc_final: 0.8171 (tmm-80) REVERT: N 108 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7821 (tm-30) REVERT: O 108 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7844 (tm-30) REVERT: P 108 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7661 (tm-30) REVERT: P 114 GLN cc_start: 0.8235 (tt0) cc_final: 0.6903 (tt0) REVERT: Q 14 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: Q 108 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7626 (tm-30) REVERT: R 96 GLU cc_start: 0.7034 (tt0) cc_final: 0.6745 (tt0) REVERT: R 108 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7777 (tm-30) REVERT: T 108 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7656 (tm-30) REVERT: V 108 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7638 (tm-30) REVERT: W 108 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7641 (tm-30) REVERT: X 108 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7881 (tm-30) REVERT: Y 108 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7722 (tm-30) REVERT: Z 108 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7478 (tm-30) REVERT: AA 108 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7655 (tm-30) REVERT: BA 108 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7657 (tm-30) REVERT: BA 109 ARG cc_start: 0.8482 (tmm-80) cc_final: 0.8157 (tmm-80) REVERT: CA 108 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7762 (tm-30) REVERT: EA 87 ARG cc_start: 0.7535 (ttm110) cc_final: 0.7222 (mtm110) REVERT: EA 108 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7557 (tm-30) REVERT: FA 108 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7672 (tm-30) REVERT: GA 108 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7672 (tm-30) REVERT: HA 108 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7709 (tm-30) REVERT: JA 108 GLN cc_start: 0.8169 (tm-30) cc_final: 0.7868 (tm-30) REVERT: LA 108 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7602 (tm-30) REVERT: LA 109 ARG cc_start: 0.8458 (tmm-80) cc_final: 0.8138 (tmm-80) REVERT: MA 110 MET cc_start: 0.8476 (tmm) cc_final: 0.7845 (ttm) REVERT: NA 108 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7686 (tm-30) REVERT: OA 108 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7589 (tm-30) REVERT: PA 108 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7642 (tm-30) REVERT: QA 108 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7621 (tm-30) REVERT: RA 96 GLU cc_start: 0.7214 (tt0) cc_final: 0.6888 (tt0) REVERT: RA 108 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7761 (tm-30) REVERT: TA 108 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7874 (tm-30) REVERT: UA 108 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7581 (tm-30) REVERT: VA 108 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7555 (tm-30) REVERT: VA 109 ARG cc_start: 0.8465 (tmm-80) cc_final: 0.8200 (tmm-80) REVERT: WA 96 GLU cc_start: 0.7262 (tt0) cc_final: 0.6711 (tt0) REVERT: WA 108 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7766 (tm-30) REVERT: YA 108 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7585 (tm-30) REVERT: ZA 108 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7869 (tm-30) REVERT: AB 108 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7607 (tm-30) REVERT: CB 108 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7740 (tm-30) REVERT: EB 108 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7667 (tm-30) REVERT: FB 108 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7616 (tm-30) REVERT: FB 109 ARG cc_start: 0.8472 (tmm-80) cc_final: 0.8153 (tmm-80) REVERT: GB 108 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7789 (tm-30) REVERT: HB 108 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7762 (tm-30) REVERT: IB 108 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7489 (tm-30) outliers start: 106 outliers final: 85 residues processed: 1058 average time/residue: 0.5874 time to fit residues: 1012.4576 Evaluate side-chains 1008 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 921 time to evaluate : 5.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 87 ARG Chi-restraints excluded: chain Q residue 14 ASP Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain T residue 70 THR Chi-restraints excluded: chain T residue 94 VAL Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain Y residue 123 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 123 LEU Chi-restraints excluded: chain BA residue 70 THR Chi-restraints excluded: chain BA residue 123 LEU Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain DA residue 94 VAL Chi-restraints excluded: chain DA residue 123 LEU Chi-restraints excluded: chain EA residue 70 THR Chi-restraints excluded: chain EA residue 94 VAL Chi-restraints excluded: chain GA residue 70 THR Chi-restraints excluded: chain GA residue 123 LEU Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 94 VAL Chi-restraints excluded: chain IA residue 123 LEU Chi-restraints excluded: chain JA residue 70 THR Chi-restraints excluded: chain JA residue 87 ARG Chi-restraints excluded: chain KA residue 123 LEU Chi-restraints excluded: chain LA residue 70 THR Chi-restraints excluded: chain LA residue 123 LEU Chi-restraints excluded: chain LA residue 127 GLN Chi-restraints excluded: chain MA residue 70 THR Chi-restraints excluded: chain NA residue 123 LEU Chi-restraints excluded: chain OA residue 70 THR Chi-restraints excluded: chain OA residue 94 VAL Chi-restraints excluded: chain QA residue 70 THR Chi-restraints excluded: chain QA residue 123 LEU Chi-restraints excluded: chain RA residue 70 THR Chi-restraints excluded: chain SA residue 127 GLN Chi-restraints excluded: chain TA residue 28 ILE Chi-restraints excluded: chain TA residue 87 ARG Chi-restraints excluded: chain TA residue 94 VAL Chi-restraints excluded: chain VA residue 70 THR Chi-restraints excluded: chain VA residue 123 LEU Chi-restraints excluded: chain VA residue 127 GLN Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain XA residue 70 THR Chi-restraints excluded: chain XA residue 94 VAL Chi-restraints excluded: chain XA residue 123 LEU Chi-restraints excluded: chain YA residue 70 THR Chi-restraints excluded: chain YA residue 94 VAL Chi-restraints excluded: chain AB residue 70 THR Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 123 LEU Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain CB residue 123 LEU Chi-restraints excluded: chain DB residue 70 THR Chi-restraints excluded: chain EB residue 123 LEU Chi-restraints excluded: chain FB residue 70 THR Chi-restraints excluded: chain FB residue 123 LEU Chi-restraints excluded: chain GB residue 70 THR Chi-restraints excluded: chain HB residue 123 LEU Chi-restraints excluded: chain IB residue 70 THR Chi-restraints excluded: chain IB residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 2.9990 chunk 395 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 518 optimal weight: 6.9990 chunk 287 optimal weight: 20.0000 chunk 593 optimal weight: 2.9990 chunk 481 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 355 optimal weight: 0.9980 chunk 624 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN G 132 GLN H 132 GLN L 132 GLN O 132 GLN Q 132 GLN W 132 GLN AA 114 GLN BA 132 GLN EA 114 GLN FA 114 GLN GA 132 GLN LA 132 GLN MA 132 GLN QA 132 GLN RA 124 GLN VA 132 GLN WA 132 GLN FB 132 GLN HB 132 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 60660 Z= 0.216 Angle : 0.471 4.776 81540 Z= 0.245 Chirality : 0.043 0.171 9780 Planarity : 0.003 0.028 10380 Dihedral : 3.380 11.748 7740 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.54 % Allowed : 20.38 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.10), residues: 7140 helix: 3.93 (0.07), residues: 3300 sheet: 0.29 (0.15), residues: 1320 loop : -1.26 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRPWA 52 HIS 0.002 0.000 HIS Y 85 PHE 0.006 0.001 PHE R 32 TYR 0.006 0.001 TYRDB 82 ARG 0.006 0.001 ARGGA 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 967 time to evaluate : 6.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7673 (tm-30) REVERT: C 96 GLU cc_start: 0.7256 (tt0) cc_final: 0.7043 (tt0) REVERT: C 108 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8096 (tm-30) REVERT: E 108 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7860 (tm-30) REVERT: F 108 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7933 (tm-30) REVERT: G 108 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7677 (tm-30) REVERT: H 108 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7782 (tm-30) REVERT: J 108 GLN cc_start: 0.8180 (tm-30) cc_final: 0.7905 (tm-30) REVERT: L 108 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7641 (tm-30) REVERT: M 108 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7761 (tm-30) REVERT: N 108 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7827 (tm-30) REVERT: O 108 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7849 (tm-30) REVERT: P 108 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7644 (tm-30) REVERT: Q 108 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7638 (tm-30) REVERT: R 96 GLU cc_start: 0.7012 (tt0) cc_final: 0.6727 (tt0) REVERT: R 108 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7810 (tm-30) REVERT: T 108 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7663 (tm-30) REVERT: V 108 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7636 (tm-30) REVERT: W 108 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7677 (tm-30) REVERT: X 60 GLU cc_start: 0.8071 (pm20) cc_final: 0.7853 (pt0) REVERT: Y 108 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7722 (tm-30) REVERT: Z 108 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7881 (tm-30) REVERT: AA 108 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7977 (tm-30) REVERT: AA 114 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: BA 108 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7655 (tm-30) REVERT: BA 109 ARG cc_start: 0.8470 (tmm-80) cc_final: 0.8145 (tmm-80) REVERT: CA 108 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7805 (tm-30) REVERT: EA 87 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7156 (mtm110) REVERT: EA 108 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7581 (tm-30) REVERT: FA 108 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7667 (tm-30) REVERT: GA 108 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7690 (tm-30) REVERT: HA 108 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7700 (tm-30) REVERT: JA 108 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7869 (tm-30) REVERT: LA 108 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7629 (tm-30) REVERT: MA 108 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7788 (tm-30) REVERT: MA 110 MET cc_start: 0.8460 (tmm) cc_final: 0.7820 (ttm) REVERT: NA 108 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7684 (tm-30) REVERT: OA 108 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7913 (tm-30) REVERT: PA 108 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7627 (tm-30) REVERT: QA 108 GLN cc_start: 0.8247 (tm-30) cc_final: 0.7650 (tm-30) REVERT: RA 108 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7778 (tm-30) REVERT: TA 108 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7878 (tm-30) REVERT: UA 108 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7573 (tm-30) REVERT: VA 108 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7677 (tm-30) REVERT: VA 109 ARG cc_start: 0.8460 (tmm-80) cc_final: 0.8110 (tmm-80) REVERT: WA 108 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7795 (tm-30) REVERT: YA 87 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7174 (mtm110) REVERT: YA 108 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7578 (tm-30) REVERT: ZA 108 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7900 (tm-30) REVERT: AB 108 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7629 (tm-30) REVERT: CB 108 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7740 (tm-30) REVERT: DB 108 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7615 (tm-30) REVERT: EB 108 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7656 (tm-30) REVERT: FB 108 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7644 (tm-30) REVERT: GB 108 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7791 (tm-30) REVERT: HB 108 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7772 (tm-30) REVERT: IB 108 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7869 (tm-30) outliers start: 109 outliers final: 78 residues processed: 1037 average time/residue: 0.5838 time to fit residues: 989.0076 Evaluate side-chains 986 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 907 time to evaluate : 5.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain T residue 94 VAL Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain W residue 70 THR Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain W residue 127 GLN Chi-restraints excluded: chain X residue 18 ASN Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain Y residue 123 LEU Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain AA residue 114 GLN Chi-restraints excluded: chain BA residue 123 LEU Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain DA residue 70 THR Chi-restraints excluded: chain DA residue 94 VAL Chi-restraints excluded: chain DA residue 123 LEU Chi-restraints excluded: chain EA residue 57 ASP Chi-restraints excluded: chain EA residue 94 VAL Chi-restraints excluded: chain GA residue 70 THR Chi-restraints excluded: chain GA residue 123 LEU Chi-restraints excluded: chain GA residue 127 GLN Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 94 VAL Chi-restraints excluded: chain IA residue 123 LEU Chi-restraints excluded: chain KA residue 123 LEU Chi-restraints excluded: chain LA residue 70 THR Chi-restraints excluded: chain LA residue 123 LEU Chi-restraints excluded: chain MA residue 70 THR Chi-restraints excluded: chain NA residue 123 LEU Chi-restraints excluded: chain OA residue 70 THR Chi-restraints excluded: chain OA residue 94 VAL Chi-restraints excluded: chain PA residue 123 LEU Chi-restraints excluded: chain QA residue 70 THR Chi-restraints excluded: chain QA residue 123 LEU Chi-restraints excluded: chain RA residue 70 THR Chi-restraints excluded: chain SA residue 123 LEU Chi-restraints excluded: chain SA residue 127 GLN Chi-restraints excluded: chain TA residue 87 ARG Chi-restraints excluded: chain TA residue 94 VAL Chi-restraints excluded: chain UA residue 123 LEU Chi-restraints excluded: chain VA residue 70 THR Chi-restraints excluded: chain VA residue 123 LEU Chi-restraints excluded: chain VA residue 127 GLN Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain XA residue 94 VAL Chi-restraints excluded: chain XA residue 123 LEU Chi-restraints excluded: chain YA residue 94 VAL Chi-restraints excluded: chain AB residue 70 THR Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 123 LEU Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain CB residue 123 LEU Chi-restraints excluded: chain DB residue 57 ASP Chi-restraints excluded: chain DB residue 70 THR Chi-restraints excluded: chain EB residue 123 LEU Chi-restraints excluded: chain FB residue 70 THR Chi-restraints excluded: chain FB residue 123 LEU Chi-restraints excluded: chain HB residue 123 LEU Chi-restraints excluded: chain IB residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 9.9990 chunk 626 optimal weight: 0.6980 chunk 137 optimal weight: 7.9990 chunk 408 optimal weight: 0.9990 chunk 171 optimal weight: 0.2980 chunk 696 optimal weight: 0.8980 chunk 578 optimal weight: 7.9990 chunk 322 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 230 optimal weight: 0.0670 chunk 365 optimal weight: 7.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN F 114 GLN F 132 GLN G 132 GLN L 132 GLN P 114 GLN Q 132 GLN W 132 GLN AA 114 GLN BA 132 GLN FA 114 GLN GA 132 GLN LA 132 GLN QA 132 GLN VA 132 GLN EB 132 GLN FB 132 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 60660 Z= 0.146 Angle : 0.453 5.570 81540 Z= 0.232 Chirality : 0.043 0.175 9780 Planarity : 0.002 0.024 10380 Dihedral : 3.133 11.320 7740 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.06 % Allowed : 21.54 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.10), residues: 7140 helix: 4.46 (0.07), residues: 3300 sheet: -0.38 (0.15), residues: 1020 loop : -0.73 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 52 HIS 0.001 0.000 HIS Y 85 PHE 0.002 0.000 PHE Q 32 TYR 0.004 0.001 TYRDB 82 ARG 0.006 0.001 ARGDB 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 1134 time to evaluate : 5.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 109 ARG cc_start: 0.8197 (tmm-80) cc_final: 0.7985 (tmm-80) REVERT: B 108 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7682 (tm-30) REVERT: C 108 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8077 (tm-30) REVERT: E 108 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7488 (tm-30) REVERT: F 108 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7633 (tm-30) REVERT: G 108 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7669 (tm-30) REVERT: G 109 ARG cc_start: 0.8391 (tmm-80) cc_final: 0.8103 (tmm-80) REVERT: H 108 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7838 (tm-30) REVERT: J 108 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7906 (tm-30) REVERT: K 108 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7621 (tm-30) REVERT: L 108 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7610 (tm-30) REVERT: L 124 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7399 (mm-40) REVERT: M 108 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7841 (tm-30) REVERT: N 108 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7789 (tm-30) REVERT: O 108 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7499 (tm-30) REVERT: P 108 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7658 (tm-30) REVERT: P 114 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7210 (tt0) REVERT: Q 108 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7662 (tm-30) REVERT: Q 109 ARG cc_start: 0.8373 (tmm-80) cc_final: 0.8100 (tmm-80) REVERT: R 108 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8133 (tm-30) REVERT: T 87 ARG cc_start: 0.7394 (ttm110) cc_final: 0.7120 (mtm110) REVERT: T 108 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7677 (tm-30) REVERT: T 109 ARG cc_start: 0.8273 (tmm-80) cc_final: 0.8043 (tmm-80) REVERT: V 57 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7435 (t0) REVERT: V 108 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7600 (tm-30) REVERT: W 108 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7638 (tm-30) REVERT: W 109 ARG cc_start: 0.8359 (tmm-80) cc_final: 0.8110 (tmm-80) REVERT: X 108 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7921 (tm-30) REVERT: Y 108 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7710 (tm-30) REVERT: Z 108 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7550 (tm-30) REVERT: AA 99 ARG cc_start: 0.8488 (tmm-80) cc_final: 0.8274 (tmm-80) REVERT: AA 108 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7548 (tm-30) REVERT: AA 109 ARG cc_start: 0.8278 (tmm-80) cc_final: 0.8004 (tmm-80) REVERT: BA 108 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7642 (tm-30) REVERT: BA 109 ARG cc_start: 0.8339 (tmm-80) cc_final: 0.7971 (tmm-80) REVERT: CA 108 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8115 (tm-30) REVERT: EA 87 ARG cc_start: 0.7369 (ttm110) cc_final: 0.7108 (mtm110) REVERT: EA 108 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7563 (tm-30) REVERT: FA 108 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7628 (tm-30) REVERT: FA 109 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.8042 (tmm-80) REVERT: GA 108 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7672 (tm-30) REVERT: HA 108 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8093 (tm-30) REVERT: JA 108 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7890 (tm-30) REVERT: LA 108 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7607 (tm-30) REVERT: LA 124 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7399 (mm-40) REVERT: MA 108 GLN cc_start: 0.8289 (tm-30) cc_final: 0.8067 (tm-30) REVERT: MA 110 MET cc_start: 0.8397 (tmm) cc_final: 0.7751 (ttm) REVERT: NA 108 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7667 (tm-30) REVERT: OA 3 ASN cc_start: 0.8156 (t0) cc_final: 0.7912 (t0) REVERT: OA 108 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7561 (tm-30) REVERT: OA 109 ARG cc_start: 0.8326 (tmm-80) cc_final: 0.8087 (tmm-80) REVERT: PA 108 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7581 (tm-30) REVERT: QA 108 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7646 (tm-30) REVERT: RA 96 GLU cc_start: 0.7211 (tt0) cc_final: 0.6795 (tt0) REVERT: RA 108 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7810 (tm-30) REVERT: TA 108 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7558 (tm-30) REVERT: TA 129 ARG cc_start: 0.7954 (mmm160) cc_final: 0.7426 (mmm160) REVERT: UA 108 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7555 (tm-30) REVERT: UA 109 ARG cc_start: 0.8228 (tmm-80) cc_final: 0.7981 (tmm-80) REVERT: VA 108 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7656 (tm-30) REVERT: VA 109 ARG cc_start: 0.8306 (tmm-80) cc_final: 0.8002 (tmm-80) REVERT: VA 124 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7425 (mm-40) REVERT: WA 108 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7832 (tm-30) REVERT: YA 87 ARG cc_start: 0.7404 (ttm110) cc_final: 0.7126 (mtm110) REVERT: YA 108 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7582 (tm-30) REVERT: YA 109 ARG cc_start: 0.8317 (tmm-80) cc_final: 0.8086 (tmm-80) REVERT: ZA 108 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7582 (tm-30) REVERT: AB 108 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7628 (tm-30) REVERT: CB 108 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7723 (tm-30) REVERT: CB 109 ARG cc_start: 0.8233 (tmm-80) cc_final: 0.7977 (tmm-80) REVERT: DB 87 ARG cc_start: 0.7485 (ttm110) cc_final: 0.7232 (mtm110) REVERT: DB 108 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7879 (tm-30) REVERT: EB 108 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7575 (tm-30) REVERT: FB 108 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7619 (tm-30) REVERT: FB 124 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7451 (mm-40) REVERT: GB 108 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7848 (tm-30) REVERT: HB 108 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7799 (tm-30) REVERT: HB 109 ARG cc_start: 0.8168 (tmm-80) cc_final: 0.7956 (tmm-80) REVERT: IB 108 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7519 (tm-30) outliers start: 75 outliers final: 44 residues processed: 1181 average time/residue: 0.6196 time to fit residues: 1168.5008 Evaluate side-chains 1003 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 957 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 114 GLN Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain Y residue 123 LEU Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain AA residue 123 LEU Chi-restraints excluded: chain BA residue 123 LEU Chi-restraints excluded: chain DA residue 123 LEU Chi-restraints excluded: chain EA residue 57 ASP Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain FA residue 123 LEU Chi-restraints excluded: chain GA residue 123 LEU Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain KA residue 123 LEU Chi-restraints excluded: chain LA residue 123 LEU Chi-restraints excluded: chain NA residue 123 LEU Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 123 LEU Chi-restraints excluded: chain SA residue 70 THR Chi-restraints excluded: chain TA residue 87 ARG Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain VA residue 11 THR Chi-restraints excluded: chain VA residue 123 LEU Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain ZA residue 123 LEU Chi-restraints excluded: chain AB residue 123 LEU Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain EB residue 123 LEU Chi-restraints excluded: chain FB residue 123 LEU Chi-restraints excluded: chain GB residue 70 THR Chi-restraints excluded: chain HB residue 123 LEU Chi-restraints excluded: chain HB residue 125 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 671 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 396 optimal weight: 7.9990 chunk 508 optimal weight: 2.9990 chunk 394 optimal weight: 5.9990 chunk 586 optimal weight: 10.0000 chunk 389 optimal weight: 10.0000 chunk 693 optimal weight: 6.9990 chunk 434 optimal weight: 9.9990 chunk 423 optimal weight: 0.5980 chunk 320 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN C 132 GLN F 132 GLN G 132 GLN L 132 GLN M 132 GLN Q 132 GLN R 132 GLN W 132 GLN BA 132 GLN CA 132 GLN GA 132 GLN LA 132 GLN PA 114 GLN QA 132 GLN RA 132 GLN VA 132 GLN AB 114 GLN EB 132 GLN FB 132 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 60660 Z= 0.211 Angle : 0.497 6.221 81540 Z= 0.257 Chirality : 0.043 0.169 9780 Planarity : 0.003 0.023 10380 Dihedral : 3.221 10.906 7740 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.16 % Allowed : 22.99 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.10), residues: 7140 helix: 4.30 (0.07), residues: 3300 sheet: 0.41 (0.15), residues: 1320 loop : -1.28 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP R 52 HIS 0.002 0.000 HIS Y 85 PHE 0.005 0.001 PHEGA 32 TYR 0.006 0.001 TYR T 82 ARG 0.006 0.001 ARGXA 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 968 time to evaluate : 5.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7634 (tm-30) REVERT: C 87 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7168 (ptp90) REVERT: C 108 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8093 (tm-30) REVERT: E 108 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7571 (tm-30) REVERT: F 108 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7928 (tm-30) REVERT: G 108 GLN cc_start: 0.8282 (tm-30) cc_final: 0.7639 (tm-30) REVERT: G 109 ARG cc_start: 0.8389 (tmm-80) cc_final: 0.8147 (tmm-80) REVERT: H 87 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7183 (ptp90) REVERT: H 108 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8115 (tm-30) REVERT: J 108 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7591 (tm-30) REVERT: L 108 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7574 (tm-30) REVERT: M 87 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7162 (ptp90) REVERT: M 96 GLU cc_start: 0.7295 (tt0) cc_final: 0.6939 (tt0) REVERT: M 108 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8118 (tm-30) REVERT: N 108 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7751 (tm-30) REVERT: O 108 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7518 (tm-30) REVERT: P 108 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7936 (tm-30) REVERT: Q 108 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7552 (tm-30) REVERT: Q 109 ARG cc_start: 0.8421 (tmm-80) cc_final: 0.8047 (tmm-80) REVERT: R 87 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7123 (ptp90) REVERT: R 108 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8135 (tm-30) REVERT: T 108 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7663 (tm-30) REVERT: T 109 ARG cc_start: 0.8305 (tmm-80) cc_final: 0.8081 (tmm-80) REVERT: V 57 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7464 (t0) REVERT: V 108 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7952 (tm-30) REVERT: W 108 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7620 (tm-30) REVERT: W 109 ARG cc_start: 0.8405 (tmm-80) cc_final: 0.8176 (tmm-80) REVERT: X 60 GLU cc_start: 0.8018 (pm20) cc_final: 0.7774 (pt0) REVERT: Y 108 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7751 (tm-30) REVERT: Z 108 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7583 (tm-30) REVERT: AA 108 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7980 (tm-30) REVERT: BA 108 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7649 (tm-30) REVERT: BA 109 ARG cc_start: 0.8404 (tmm-80) cc_final: 0.8172 (tmm-80) REVERT: CA 87 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7163 (ptp90) REVERT: CA 108 GLN cc_start: 0.8374 (tm-30) cc_final: 0.8130 (tm-30) REVERT: EA 87 ARG cc_start: 0.7415 (ttm110) cc_final: 0.7124 (mtm110) REVERT: EA 108 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7637 (tm-30) REVERT: FA 108 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7972 (tm-30) REVERT: GA 108 GLN cc_start: 0.8291 (tm-30) cc_final: 0.7620 (tm-30) REVERT: HA 108 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8105 (tm-30) REVERT: JA 108 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7595 (tm-30) REVERT: KA 108 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7606 (tm-30) REVERT: LA 108 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7562 (tm-30) REVERT: MA 108 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8113 (tm-30) REVERT: MA 110 MET cc_start: 0.8421 (tmm) cc_final: 0.7753 (ttm) REVERT: NA 108 GLN cc_start: 0.8292 (tm-30) cc_final: 0.7698 (tm-30) REVERT: OA 108 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7639 (tm-30) REVERT: OA 109 ARG cc_start: 0.8357 (tmm-80) cc_final: 0.8128 (tmm-80) REVERT: PA 108 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7967 (tm-30) REVERT: QA 108 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7583 (tm-30) REVERT: RA 96 GLU cc_start: 0.7235 (tt0) cc_final: 0.6799 (tt0) REVERT: RA 108 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7838 (tm-30) REVERT: TA 108 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7614 (tm-30) REVERT: TA 129 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7749 (mmm160) REVERT: UA 108 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7935 (tm-30) REVERT: VA 108 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7683 (tm-30) REVERT: WA 108 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8092 (tm-30) REVERT: YA 87 ARG cc_start: 0.7451 (ttm110) cc_final: 0.7119 (mtm110) REVERT: YA 108 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7636 (tm-30) REVERT: YA 109 ARG cc_start: 0.8368 (tmm-80) cc_final: 0.8134 (tmm-80) REVERT: ZA 108 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7934 (tm-30) REVERT: AB 108 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7683 (tm-30) REVERT: BB 108 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8049 (tm-30) REVERT: CB 108 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7778 (tm-30) REVERT: CB 109 ARG cc_start: 0.8301 (tmm-80) cc_final: 0.8058 (tmm-80) REVERT: DB 87 ARG cc_start: 0.7436 (ttm110) cc_final: 0.7141 (mtm110) REVERT: DB 108 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7621 (tm-30) REVERT: EB 108 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7964 (tm-30) REVERT: FB 108 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7583 (tm-30) REVERT: GB 87 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7143 (ptp90) REVERT: GB 108 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7857 (tm-30) REVERT: HB 108 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7830 (tm-30) REVERT: HB 109 ARG cc_start: 0.8261 (tmm-80) cc_final: 0.8053 (tmm-80) REVERT: IB 108 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7593 (tm-30) outliers start: 82 outliers final: 49 residues processed: 1028 average time/residue: 0.6037 time to fit residues: 1009.3898 Evaluate side-chains 997 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 941 time to evaluate : 5.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain W residue 127 GLN Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain Y residue 123 LEU Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain AA residue 123 LEU Chi-restraints excluded: chain BA residue 123 LEU Chi-restraints excluded: chain CA residue 87 ARG Chi-restraints excluded: chain EA residue 57 ASP Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain FA residue 123 LEU Chi-restraints excluded: chain GA residue 123 LEU Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain IA residue 123 LEU Chi-restraints excluded: chain KA residue 123 LEU Chi-restraints excluded: chain LA residue 123 LEU Chi-restraints excluded: chain NA residue 123 LEU Chi-restraints excluded: chain OA residue 57 ASP Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 123 LEU Chi-restraints excluded: chain SA residue 123 LEU Chi-restraints excluded: chain TA residue 87 ARG Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain VA residue 11 THR Chi-restraints excluded: chain VA residue 123 LEU Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain ZA residue 123 LEU Chi-restraints excluded: chain AB residue 123 LEU Chi-restraints excluded: chain CB residue 123 LEU Chi-restraints excluded: chain DB residue 57 ASP Chi-restraints excluded: chain EB residue 123 LEU Chi-restraints excluded: chain FB residue 123 LEU Chi-restraints excluded: chain FB residue 127 GLN Chi-restraints excluded: chain GB residue 87 ARG Chi-restraints excluded: chain HB residue 123 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 429 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 chunk 414 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 136 optimal weight: 0.0370 chunk 134 optimal weight: 10.0000 chunk 441 optimal weight: 2.9990 chunk 472 optimal weight: 0.3980 chunk 343 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 545 optimal weight: 9.9990 overall best weight: 1.6864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN G 132 GLN L 132 GLN P 114 GLN Q 132 GLN W 132 GLN BA 132 GLN DA 23 GLN GA 132 GLN LA 132 GLN PA 114 GLN QA 132 GLN VA 132 GLN FB 132 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 60660 Z= 0.187 Angle : 0.500 6.924 81540 Z= 0.256 Chirality : 0.043 0.170 9780 Planarity : 0.003 0.027 10380 Dihedral : 3.179 10.997 7740 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.36 % Allowed : 23.01 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.10), residues: 7140 helix: 4.40 (0.07), residues: 3300 sheet: 0.44 (0.15), residues: 1320 loop : -1.29 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 52 HIS 0.002 0.000 HIS Y 85 PHE 0.004 0.001 PHEVA 32 TYR 0.005 0.001 TYR T 82 ARG 0.006 0.001 ARGLA 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1001 time to evaluate : 6.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7639 (tm-30) REVERT: B 108 GLN cc_start: 0.8245 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 110 MET cc_start: 0.8588 (tmm) cc_final: 0.8363 (tmm) REVERT: C 87 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7052 (ptp90) REVERT: C 108 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8024 (tm-30) REVERT: E 108 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7581 (tm-30) REVERT: F 108 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7910 (tm-30) REVERT: G 108 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7607 (tm-30) REVERT: G 109 ARG cc_start: 0.8384 (tmm-80) cc_final: 0.8137 (tmm-80) REVERT: G 110 MET cc_start: 0.8584 (tmm) cc_final: 0.8354 (tmm) REVERT: H 108 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8105 (tm-30) REVERT: J 108 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7566 (tm-30) REVERT: K 108 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7668 (tm-30) REVERT: L 108 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7530 (tm-30) REVERT: L 110 MET cc_start: 0.8607 (tmm) cc_final: 0.8382 (tmm) REVERT: L 124 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7404 (mm-40) REVERT: M 87 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7040 (ptp90) REVERT: M 96 GLU cc_start: 0.7240 (tt0) cc_final: 0.6898 (tt0) REVERT: M 108 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8109 (tm-30) REVERT: N 108 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7743 (tm-30) REVERT: O 108 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7507 (tm-30) REVERT: P 108 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7918 (tm-30) REVERT: Q 108 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7568 (tm-30) REVERT: Q 109 ARG cc_start: 0.8392 (tmm-80) cc_final: 0.8166 (tmm-80) REVERT: R 87 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7070 (ptp90) REVERT: R 108 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8113 (tm-30) REVERT: T 87 ARG cc_start: 0.7391 (ttm110) cc_final: 0.7107 (mtm110) REVERT: T 108 GLN cc_start: 0.8260 (tm-30) cc_final: 0.7661 (tm-30) REVERT: T 109 ARG cc_start: 0.8289 (tmm-80) cc_final: 0.8068 (tmm-80) REVERT: V 57 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7465 (t0) REVERT: V 108 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7941 (tm-30) REVERT: W 108 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7571 (tm-30) REVERT: W 109 ARG cc_start: 0.8379 (tmm-80) cc_final: 0.8144 (tmm-80) REVERT: W 110 MET cc_start: 0.8593 (tmm) cc_final: 0.8381 (tmm) REVERT: X 60 GLU cc_start: 0.8040 (pm20) cc_final: 0.7793 (pt0) REVERT: Y 108 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7764 (tm-30) REVERT: Z 108 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7591 (tm-30) REVERT: AA 3 ASN cc_start: 0.8068 (t0) cc_final: 0.7795 (t0) REVERT: AA 108 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7984 (tm-30) REVERT: BA 108 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7628 (tm-30) REVERT: BA 109 ARG cc_start: 0.8366 (tmm-80) cc_final: 0.8046 (tmm-80) REVERT: CA 87 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7093 (ptp90) REVERT: CA 108 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8097 (tm-30) REVERT: EA 87 ARG cc_start: 0.7391 (ttm110) cc_final: 0.7102 (mtm110) REVERT: EA 108 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7611 (tm-30) REVERT: FA 108 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7682 (tm-30) REVERT: FA 109 ARG cc_start: 0.8326 (tmm-80) cc_final: 0.8080 (tmm-80) REVERT: GA 108 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7601 (tm-30) REVERT: GA 110 MET cc_start: 0.8588 (tmm) cc_final: 0.8361 (tmm) REVERT: HA 108 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8070 (tm-30) REVERT: JA 108 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7915 (tm-30) REVERT: LA 108 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7525 (tm-30) REVERT: LA 110 MET cc_start: 0.8603 (tmm) cc_final: 0.8380 (tmm) REVERT: MA 108 GLN cc_start: 0.8315 (tm-30) cc_final: 0.8059 (tm-30) REVERT: MA 110 MET cc_start: 0.8414 (tmm) cc_final: 0.7748 (ttm) REVERT: NA 108 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7698 (tm-30) REVERT: OA 3 ASN cc_start: 0.8117 (t0) cc_final: 0.7864 (t0) REVERT: OA 108 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7938 (tm-30) REVERT: PA 108 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7973 (tm-30) REVERT: QA 108 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7551 (tm-30) REVERT: QA 110 MET cc_start: 0.8604 (tmm) cc_final: 0.8386 (tmm) REVERT: RA 108 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8047 (tm-30) REVERT: TA 108 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7600 (tm-30) REVERT: UA 108 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7911 (tm-30) REVERT: VA 108 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7670 (tm-30) REVERT: WA 108 GLN cc_start: 0.8345 (tm-30) cc_final: 0.8045 (tm-30) REVERT: YA 87 ARG cc_start: 0.7416 (ttm110) cc_final: 0.7105 (mtm110) REVERT: YA 108 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7645 (tm-30) REVERT: YA 109 ARG cc_start: 0.8338 (tmm-80) cc_final: 0.8121 (tmm-80) REVERT: ZA 108 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7919 (tm-30) REVERT: ZA 110 MET cc_start: 0.8567 (tmm) cc_final: 0.8340 (tmm) REVERT: AB 108 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7648 (tm-30) REVERT: AB 110 MET cc_start: 0.8554 (tmm) cc_final: 0.8339 (tmm) REVERT: BB 96 GLU cc_start: 0.7246 (tt0) cc_final: 0.6837 (tt0) REVERT: BB 108 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8025 (tm-30) REVERT: CB 108 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7761 (tm-30) REVERT: CB 109 ARG cc_start: 0.8284 (tmm-80) cc_final: 0.8059 (tmm-80) REVERT: DB 87 ARG cc_start: 0.7373 (ttm110) cc_final: 0.7083 (mtm110) REVERT: DB 108 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7614 (tm-30) REVERT: EB 108 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7962 (tm-30) REVERT: FB 108 GLN cc_start: 0.8211 (tm-30) cc_final: 0.7555 (tm-30) REVERT: FB 110 MET cc_start: 0.8595 (tmm) cc_final: 0.8372 (tmm) REVERT: FB 124 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7432 (mm-40) REVERT: GB 87 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7028 (ptp90) REVERT: GB 96 GLU cc_start: 0.7156 (tt0) cc_final: 0.6751 (tt0) REVERT: GB 108 GLN cc_start: 0.8367 (tm-30) cc_final: 0.8106 (tm-30) REVERT: HB 108 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7814 (tm-30) REVERT: HB 109 ARG cc_start: 0.8234 (tmm-80) cc_final: 0.8029 (tmm-80) REVERT: IB 108 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7589 (tm-30) outliers start: 96 outliers final: 63 residues processed: 1073 average time/residue: 0.6263 time to fit residues: 1082.8245 Evaluate side-chains 1021 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 952 time to evaluate : 5.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain T residue 57 ASP Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain Y residue 123 LEU Chi-restraints excluded: chain Z residue 87 ARG Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain AA residue 123 LEU Chi-restraints excluded: chain BA residue 123 LEU Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 87 ARG Chi-restraints excluded: chain CA residue 123 LEU Chi-restraints excluded: chain DA residue 123 LEU Chi-restraints excluded: chain EA residue 57 ASP Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain FA residue 123 LEU Chi-restraints excluded: chain GA residue 123 LEU Chi-restraints excluded: chain GA residue 127 GLN Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain KA residue 123 LEU Chi-restraints excluded: chain LA residue 98 LEU Chi-restraints excluded: chain LA residue 123 LEU Chi-restraints excluded: chain NA residue 11 THR Chi-restraints excluded: chain OA residue 57 ASP Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 98 LEU Chi-restraints excluded: chain QA residue 123 LEU Chi-restraints excluded: chain TA residue 87 ARG Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 123 LEU Chi-restraints excluded: chain VA residue 11 THR Chi-restraints excluded: chain VA residue 123 LEU Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain YA residue 57 ASP Chi-restraints excluded: chain ZA residue 123 LEU Chi-restraints excluded: chain AB residue 123 LEU Chi-restraints excluded: chain CB residue 123 LEU Chi-restraints excluded: chain DB residue 68 VAL Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain EB residue 123 LEU Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain FB residue 123 LEU Chi-restraints excluded: chain GB residue 87 ARG Chi-restraints excluded: chain HB residue 123 LEU Chi-restraints excluded: chain HB residue 125 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 631 optimal weight: 3.9990 chunk 664 optimal weight: 9.9990 chunk 606 optimal weight: 10.0000 chunk 646 optimal weight: 6.9990 chunk 389 optimal weight: 4.9990 chunk 281 optimal weight: 6.9990 chunk 507 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 584 optimal weight: 5.9990 chunk 611 optimal weight: 5.9990 chunk 644 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN C 132 GLN D 23 GLN G 132 GLN H 132 GLN L 132 GLN M 132 GLN Q 132 GLN W 132 GLN BA 132 GLN CA 132 GLN DA 114 GLN GA 132 GLN LA 132 GLN QA 132 GLN VA 132 GLN FB 132 GLN GB 114 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 60660 Z= 0.306 Angle : 0.564 6.728 81540 Z= 0.294 Chirality : 0.044 0.169 9780 Planarity : 0.003 0.027 10380 Dihedral : 3.521 12.061 7740 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.91 % Allowed : 23.32 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.10), residues: 7140 helix: 3.89 (0.07), residues: 3300 sheet: 0.21 (0.14), residues: 1320 loop : -1.24 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRPDB 52 HIS 0.003 0.000 HIS Y 85 PHE 0.009 0.002 PHE H 32 TYR 0.008 0.001 TYR T 82 ARG 0.006 0.001 ARGBA 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 957 time to evaluate : 6.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 87 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7124 (ttp80) REVERT: C 96 GLU cc_start: 0.7200 (tt0) cc_final: 0.6826 (tt0) REVERT: C 108 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7995 (tm-30) REVERT: E 108 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7635 (tm-30) REVERT: F 108 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7950 (tm-30) REVERT: G 108 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7588 (tm-30) REVERT: G 109 ARG cc_start: 0.8484 (tmm-80) cc_final: 0.8176 (tmm-80) REVERT: H 87 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7137 (ttp80) REVERT: H 108 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8118 (tm-30) REVERT: J 108 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7628 (tm-30) REVERT: L 108 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7556 (tm-30) REVERT: M 87 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7106 (ttp80) REVERT: M 108 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8101 (tm-30) REVERT: N 108 GLN cc_start: 0.8330 (tm-30) cc_final: 0.7761 (tm-30) REVERT: O 108 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7566 (tm-30) REVERT: P 108 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7946 (tm-30) REVERT: Q 108 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7594 (tm-30) REVERT: Q 109 ARG cc_start: 0.8491 (tmm-80) cc_final: 0.8124 (tmm-80) REVERT: R 87 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7087 (ttp80) REVERT: R 108 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8110 (tm-30) REVERT: T 108 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7658 (tm-30) REVERT: V 57 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7593 (t0) REVERT: V 108 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8034 (tm-30) REVERT: W 108 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7593 (tm-30) REVERT: W 109 ARG cc_start: 0.8472 (tmm-80) cc_final: 0.8217 (tmm-80) REVERT: Y 108 GLN cc_start: 0.8349 (tm-30) cc_final: 0.7779 (tm-30) REVERT: Z 108 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7652 (tm-30) REVERT: AA 108 GLN cc_start: 0.8319 (tm-30) cc_final: 0.8018 (tm-30) REVERT: BA 108 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7705 (tm-30) REVERT: BA 109 ARG cc_start: 0.8484 (tmm-80) cc_final: 0.8208 (tmm-80) REVERT: CA 87 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7123 (ttp80) REVERT: CA 108 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8098 (tm-30) REVERT: EA 108 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7674 (tm-30) REVERT: FA 108 GLN cc_start: 0.8326 (tm-30) cc_final: 0.8013 (tm-30) REVERT: GA 108 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7622 (tm-30) REVERT: HA 108 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8078 (tm-30) REVERT: JA 108 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7632 (tm-30) REVERT: KA 108 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7702 (tm-30) REVERT: LA 108 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7546 (tm-30) REVERT: MA 96 GLU cc_start: 0.7263 (tt0) cc_final: 0.6845 (tt0) REVERT: MA 108 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8045 (tm-30) REVERT: MA 110 MET cc_start: 0.8468 (tmm) cc_final: 0.7824 (ttm) REVERT: NA 98 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8404 (tp) REVERT: NA 108 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7734 (tm-30) REVERT: OA 108 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7614 (tm-30) REVERT: PA 108 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8022 (tm-30) REVERT: QA 108 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7571 (tm-30) REVERT: RA 96 GLU cc_start: 0.7200 (tt0) cc_final: 0.6741 (tt0) REVERT: RA 108 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8053 (tm-30) REVERT: TA 108 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7632 (tm-30) REVERT: UA 108 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7967 (tm-30) REVERT: VA 108 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7708 (tm-30) REVERT: WA 96 GLU cc_start: 0.7180 (tt0) cc_final: 0.6942 (tt0) REVERT: WA 108 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8030 (tm-30) REVERT: YA 108 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7674 (tm-30) REVERT: YA 109 ARG cc_start: 0.8440 (tmm-80) cc_final: 0.8193 (tmm-80) REVERT: ZA 108 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8022 (tm-30) REVERT: AB 108 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7702 (tm-30) REVERT: BB 108 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8060 (tm-30) REVERT: CB 108 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7825 (tm-30) REVERT: CB 109 ARG cc_start: 0.8372 (tmm-80) cc_final: 0.8128 (tmm-80) REVERT: DB 108 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7639 (tm-30) REVERT: EB 108 GLN cc_start: 0.8315 (tm-30) cc_final: 0.8004 (tm-30) REVERT: FB 108 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7560 (tm-30) REVERT: GB 87 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7125 (ttp80) REVERT: GB 108 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8089 (tm-30) REVERT: HB 99 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8322 (ttp80) REVERT: HB 108 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7810 (tm-30) REVERT: HB 109 ARG cc_start: 0.8318 (tmm-80) cc_final: 0.8077 (tmm-80) REVERT: IB 108 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7645 (tm-30) outliers start: 135 outliers final: 96 residues processed: 1055 average time/residue: 0.5860 time to fit residues: 1012.3777 Evaluate side-chains 1035 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 931 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain T residue 57 ASP Chi-restraints excluded: chain T residue 94 VAL Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain W residue 127 GLN Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain Y residue 123 LEU Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 98 LEU Chi-restraints excluded: chain BA residue 123 LEU Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 87 ARG Chi-restraints excluded: chain CA residue 123 LEU Chi-restraints excluded: chain DA residue 94 VAL Chi-restraints excluded: chain DA residue 123 LEU Chi-restraints excluded: chain EA residue 57 ASP Chi-restraints excluded: chain EA residue 68 VAL Chi-restraints excluded: chain EA residue 94 VAL Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 98 LEU Chi-restraints excluded: chain GA residue 123 LEU Chi-restraints excluded: chain GA residue 127 GLN Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 94 VAL Chi-restraints excluded: chain IA residue 123 LEU Chi-restraints excluded: chain KA residue 123 LEU Chi-restraints excluded: chain LA residue 98 LEU Chi-restraints excluded: chain LA residue 123 LEU Chi-restraints excluded: chain NA residue 11 THR Chi-restraints excluded: chain NA residue 98 LEU Chi-restraints excluded: chain NA residue 123 LEU Chi-restraints excluded: chain OA residue 57 ASP Chi-restraints excluded: chain OA residue 94 VAL Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 98 LEU Chi-restraints excluded: chain QA residue 123 LEU Chi-restraints excluded: chain TA residue 68 VAL Chi-restraints excluded: chain TA residue 87 ARG Chi-restraints excluded: chain TA residue 94 VAL Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 123 LEU Chi-restraints excluded: chain VA residue 11 THR Chi-restraints excluded: chain VA residue 70 THR Chi-restraints excluded: chain VA residue 123 LEU Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain XA residue 94 VAL Chi-restraints excluded: chain XA residue 123 LEU Chi-restraints excluded: chain YA residue 57 ASP Chi-restraints excluded: chain YA residue 94 VAL Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 123 LEU Chi-restraints excluded: chain BB residue 123 LEU Chi-restraints excluded: chain CB residue 68 VAL Chi-restraints excluded: chain CB residue 123 LEU Chi-restraints excluded: chain DB residue 57 ASP Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain EB residue 123 LEU Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain FB residue 123 LEU Chi-restraints excluded: chain FB residue 127 GLN Chi-restraints excluded: chain GB residue 70 THR Chi-restraints excluded: chain GB residue 87 ARG Chi-restraints excluded: chain HB residue 123 LEU Chi-restraints excluded: chain HB residue 125 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 424 optimal weight: 6.9990 chunk 683 optimal weight: 20.0000 chunk 417 optimal weight: 9.9990 chunk 324 optimal weight: 0.0020 chunk 475 optimal weight: 4.9990 chunk 717 optimal weight: 9.9990 chunk 660 optimal weight: 5.9990 chunk 571 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 441 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN D 23 GLN E 23 GLN G 132 GLN L 132 GLN N 23 GLN Q 132 GLN S 23 GLN T 23 GLN W 132 GLN BA 132 GLN EA 23 GLN GA 132 GLN LA 132 GLN OA 23 GLN QA 132 GLN SA 23 GLN VA 132 GLN YA 23 GLN BB 114 GLN FB 132 GLN GB 132 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 60660 Z= 0.273 Angle : 0.546 7.576 81540 Z= 0.286 Chirality : 0.044 0.166 9780 Planarity : 0.003 0.031 10380 Dihedral : 3.504 11.773 7740 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.91 % Allowed : 23.93 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.10), residues: 7140 helix: 3.88 (0.08), residues: 3300 sheet: 0.14 (0.14), residues: 1320 loop : -1.25 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRPBB 52 HIS 0.003 0.000 HIS Y 85 PHE 0.007 0.002 PHE H 32 TYR 0.006 0.001 TYR T 82 ARG 0.008 0.001 ARGDB 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14280 Ramachandran restraints generated. 7140 Oldfield, 0 Emsley, 7140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 945 time to evaluate : 6.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7612 (t0) REVERT: A 108 GLN cc_start: 0.8106 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 108 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7620 (tm-30) REVERT: C 87 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7109 (ttp80) REVERT: C 96 GLU cc_start: 0.7206 (tt0) cc_final: 0.6785 (tt0) REVERT: C 108 GLN cc_start: 0.8317 (tm-30) cc_final: 0.7620 (tm-30) REVERT: E 108 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7609 (tm-30) REVERT: F 108 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7932 (tm-30) REVERT: G 87 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7417 (mtm110) REVERT: G 108 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7594 (tm-30) REVERT: G 109 ARG cc_start: 0.8481 (tmm-80) cc_final: 0.8214 (tmm-80) REVERT: H 87 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7130 (ttp80) REVERT: H 108 GLN cc_start: 0.8377 (tm-30) cc_final: 0.8091 (tm-30) REVERT: J 108 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7898 (tm-30) REVERT: K 108 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7702 (tm-30) REVERT: L 87 ARG cc_start: 0.7631 (ttm110) cc_final: 0.7357 (mtm110) REVERT: L 108 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7560 (tm-30) REVERT: M 87 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.7099 (ttp80) REVERT: M 96 GLU cc_start: 0.7303 (tt0) cc_final: 0.6927 (tt0) REVERT: M 108 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8086 (tm-30) REVERT: N 108 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7757 (tm-30) REVERT: O 108 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7548 (tm-30) REVERT: P 108 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7914 (tm-30) REVERT: Q 87 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7419 (mtm110) REVERT: Q 108 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7586 (tm-30) REVERT: Q 109 ARG cc_start: 0.8486 (tmm-80) cc_final: 0.8224 (tmm-80) REVERT: R 87 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7098 (ttp80) REVERT: R 108 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8099 (tm-30) REVERT: T 99 ARG cc_start: 0.8370 (tmm-80) cc_final: 0.8151 (ttp80) REVERT: T 108 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7631 (tm-30) REVERT: V 57 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7629 (t0) REVERT: V 108 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7998 (tm-30) REVERT: W 87 ARG cc_start: 0.7712 (ttm110) cc_final: 0.7433 (mtm110) REVERT: W 108 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7579 (tm-30) REVERT: W 109 ARG cc_start: 0.8479 (tmm-80) cc_final: 0.8084 (tmm-80) REVERT: Y 108 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7768 (tm-30) REVERT: Z 108 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7629 (tm-30) REVERT: AA 108 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7725 (tm-30) REVERT: BA 87 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7406 (mtm110) REVERT: BA 108 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7684 (tm-30) REVERT: BA 109 ARG cc_start: 0.8501 (tmm-80) cc_final: 0.8208 (tmm-80) REVERT: CA 87 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7113 (ttp80) REVERT: CA 108 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8088 (tm-30) REVERT: EA 108 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7645 (tm-30) REVERT: FA 108 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7751 (tm-30) REVERT: GA 108 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7600 (tm-30) REVERT: HA 108 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8070 (tm-30) REVERT: JA 108 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7597 (tm-30) REVERT: LA 87 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7388 (mtm110) REVERT: LA 108 GLN cc_start: 0.8225 (tm-30) cc_final: 0.7552 (tm-30) REVERT: MA 96 GLU cc_start: 0.7251 (tt0) cc_final: 0.6858 (tt0) REVERT: MA 108 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8011 (tm-30) REVERT: MA 110 MET cc_start: 0.8453 (tmm) cc_final: 0.7825 (ttm) REVERT: NA 98 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8407 (tp) REVERT: NA 108 GLN cc_start: 0.8293 (tm-30) cc_final: 0.7727 (tm-30) REVERT: OA 108 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7594 (tm-30) REVERT: PA 57 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7635 (t0) REVERT: PA 108 GLN cc_start: 0.8315 (tm-30) cc_final: 0.8013 (tm-30) REVERT: QA 87 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7406 (mtm110) REVERT: QA 108 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7573 (tm-30) REVERT: RA 96 GLU cc_start: 0.7172 (tt0) cc_final: 0.6745 (tt0) REVERT: RA 108 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8020 (tm-30) REVERT: UA 108 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7933 (tm-30) REVERT: UA 124 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7392 (mm-40) REVERT: VA 87 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7471 (mtm110) REVERT: VA 108 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7710 (tm-30) REVERT: WA 108 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8027 (tm-30) REVERT: YA 108 GLN cc_start: 0.8277 (tm-30) cc_final: 0.7651 (tm-30) REVERT: YA 109 ARG cc_start: 0.8439 (tmm-80) cc_final: 0.8186 (tmm-80) REVERT: ZA 108 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7978 (tm-30) REVERT: AB 108 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7709 (tm-30) REVERT: BB 108 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8055 (tm-30) REVERT: CB 108 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7808 (tm-30) REVERT: CB 109 ARG cc_start: 0.8354 (tmm-80) cc_final: 0.8125 (tmm-80) REVERT: DB 108 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7626 (tm-30) REVERT: EB 108 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7740 (tm-30) REVERT: FB 87 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7402 (mtm110) REVERT: FB 108 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7557 (tm-30) REVERT: GB 87 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7095 (ttp80) REVERT: GB 108 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8069 (tm-30) REVERT: HB 108 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7796 (tm-30) REVERT: HB 109 ARG cc_start: 0.8305 (tmm-80) cc_final: 0.8078 (tmm-80) REVERT: IB 108 GLN cc_start: 0.8258 (tm-30) cc_final: 0.7617 (tm-30) outliers start: 135 outliers final: 103 residues processed: 1037 average time/residue: 0.5894 time to fit residues: 999.4347 Evaluate side-chains 1043 residues out of total 7080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 930 time to evaluate : 5.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain E residue 23 GLN Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 87 ARG Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 23 GLN Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 87 ARG Chi-restraints excluded: chain S residue 23 GLN Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain T residue 23 GLN Chi-restraints excluded: chain T residue 57 ASP Chi-restraints excluded: chain T residue 94 VAL Chi-restraints excluded: chain V residue 57 ASP Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 98 LEU Chi-restraints excluded: chain W residue 123 LEU Chi-restraints excluded: chain W residue 127 GLN Chi-restraints excluded: chain X residue 70 THR Chi-restraints excluded: chain X residue 123 LEU Chi-restraints excluded: chain Y residue 123 LEU Chi-restraints excluded: chain AA residue 68 VAL Chi-restraints excluded: chain BA residue 68 VAL Chi-restraints excluded: chain BA residue 98 LEU Chi-restraints excluded: chain BA residue 123 LEU Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 87 ARG Chi-restraints excluded: chain DA residue 94 VAL Chi-restraints excluded: chain DA residue 123 LEU Chi-restraints excluded: chain EA residue 23 GLN Chi-restraints excluded: chain EA residue 57 ASP Chi-restraints excluded: chain EA residue 68 VAL Chi-restraints excluded: chain EA residue 94 VAL Chi-restraints excluded: chain FA residue 68 VAL Chi-restraints excluded: chain GA residue 68 VAL Chi-restraints excluded: chain GA residue 98 LEU Chi-restraints excluded: chain GA residue 123 LEU Chi-restraints excluded: chain GA residue 127 GLN Chi-restraints excluded: chain HA residue 70 THR Chi-restraints excluded: chain HA residue 94 VAL Chi-restraints excluded: chain IA residue 94 VAL Chi-restraints excluded: chain IA residue 123 LEU Chi-restraints excluded: chain KA residue 123 LEU Chi-restraints excluded: chain LA residue 68 VAL Chi-restraints excluded: chain LA residue 98 LEU Chi-restraints excluded: chain LA residue 123 LEU Chi-restraints excluded: chain NA residue 11 THR Chi-restraints excluded: chain NA residue 98 LEU Chi-restraints excluded: chain NA residue 123 LEU Chi-restraints excluded: chain OA residue 23 GLN Chi-restraints excluded: chain OA residue 57 ASP Chi-restraints excluded: chain OA residue 94 VAL Chi-restraints excluded: chain PA residue 57 ASP Chi-restraints excluded: chain PA residue 68 VAL Chi-restraints excluded: chain QA residue 68 VAL Chi-restraints excluded: chain QA residue 98 LEU Chi-restraints excluded: chain QA residue 123 LEU Chi-restraints excluded: chain TA residue 68 VAL Chi-restraints excluded: chain TA residue 70 THR Chi-restraints excluded: chain TA residue 87 ARG Chi-restraints excluded: chain TA residue 94 VAL Chi-restraints excluded: chain UA residue 68 VAL Chi-restraints excluded: chain UA residue 123 LEU Chi-restraints excluded: chain VA residue 11 THR Chi-restraints excluded: chain VA residue 123 LEU Chi-restraints excluded: chain WA residue 70 THR Chi-restraints excluded: chain XA residue 94 VAL Chi-restraints excluded: chain XA residue 123 LEU Chi-restraints excluded: chain YA residue 23 GLN Chi-restraints excluded: chain YA residue 57 ASP Chi-restraints excluded: chain YA residue 94 VAL Chi-restraints excluded: chain ZA residue 68 VAL Chi-restraints excluded: chain AB residue 94 VAL Chi-restraints excluded: chain AB residue 123 LEU Chi-restraints excluded: chain CB residue 68 VAL Chi-restraints excluded: chain CB residue 123 LEU Chi-restraints excluded: chain DB residue 57 ASP Chi-restraints excluded: chain EB residue 68 VAL Chi-restraints excluded: chain EB residue 123 LEU Chi-restraints excluded: chain FB residue 98 LEU Chi-restraints excluded: chain FB residue 123 LEU Chi-restraints excluded: chain FB residue 127 GLN Chi-restraints excluded: chain GB residue 70 THR Chi-restraints excluded: chain GB residue 87 ARG Chi-restraints excluded: chain HB residue 123 LEU Chi-restraints excluded: chain HB residue 125 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 453 optimal weight: 10.0000 chunk 608 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 526 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 572 optimal weight: 8.9990 chunk 239 optimal weight: 5.9990 chunk 587 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 GLN C 132 GLN D 23 GLN L 132 GLN O 23 GLN Q 132 GLN R 132 GLN W 132 GLN Y 23 GLN Z 46 GLN BA 132 GLN CA 132 GLN GA 132 GLN LA 132 GLN QA 132 GLN VA 132 GLN FB 132 GLN GB 132 GLN IB 46 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095896 restraints weight = 73821.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096796 restraints weight = 59836.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097550 restraints weight = 51708.142| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 60660 Z= 0.284 Angle : 0.555 8.118 81540 Z= 0.290 Chirality : 0.044 0.166 9780 Planarity : 0.003 0.031 10380 Dihedral : 3.507 11.768 7740 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.95 % Allowed : 24.04 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.10), residues: 7140 helix: 3.86 (0.08), residues: 3300 sheet: 0.12 (0.14), residues: 1320 loop : -1.26 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRPBB 52 HIS 0.003 0.000 HIS Y 85 PHE 0.008 0.002 PHE H 32 TYR 0.007 0.001 TYR T 82 ARG 0.008 0.001 ARGDB 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15503.29 seconds wall clock time: 270 minutes 32.11 seconds (16232.11 seconds total)