Starting phenix.real_space_refine on Thu Aug 6 18:15:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bqw_16189/08_2026/8bqw_16189.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bqw_16189/08_2026/8bqw_16189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bqw_16189/08_2026/8bqw_16189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bqw_16189/08_2026/8bqw_16189.map" model { file = "/net/cci-nas-00/data/ceres_data/8bqw_16189/08_2026/8bqw_16189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bqw_16189/08_2026/8bqw_16189.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 10740 2.51 5 N 3060 2.21 5 O 3585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17385 Number of models: 1 Model: "" Number of chains: 90 Chain: "M" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "N" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "O" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "R" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "S" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "R" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "U" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "V" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "W" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "X" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "U" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "V" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "Z" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "0" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "1" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "Y" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "Z" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "2" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "3" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "4" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "2" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "3" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "6" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "7" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "8" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "9" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "6" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "F" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "J" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "a" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "b" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "c" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "a" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "b" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "e" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "f" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "g" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "h" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "f" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "j" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "k" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "l" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "i" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "j" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "m" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "n" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "o" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "p" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "m" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "q" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "r" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "s" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "t" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "q" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "r" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "u" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "v" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 530 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain breaks: 1 Chain: "w" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "x" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "u" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "v" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 4.17, per 1000 atoms: 0.24 Number of scatterers: 17385 At special positions: 0 Unit cell: (141.765, 90.148, 57.433, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3585 8.00 N 3060 7.00 C 10740 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 Links applied TRANS " UNK 0 6 " - " UNK G 5 " " UNK 0 9 " - " UNK G 8 " " UNK 1 6 " - " UNK H 5 " " UNK 1 7 " - " UNK H 6 " " UNK 1 9 " - " UNK H 8 " " VAL 2 16 " - " VAL M 15 " " ALA 2 18 " - " ALA M 17 " " GLU 2 20 " - " ALA M 19 " " LYS 2 21 " - " GLU M 20 " " THR 2 22 " - " LYS M 21 " " LYS 2 23 " - " THR M 22 " " GLN 2 24 " - " LYS M 23 " " GLY 2 25 " - " GLN M 24 " " VAL 2 37 " - " GLY M 36 " " LEU 2 38 " - " VAL M 37 " " TYR 2 39 " - " LEU M 38 " " VAL 2 40 " - " TYR M 39 " " GLY 2 41 " - " VAL M 40 " " SER 2 42 " - " GLY M 41 " " LYS 2 43 " - " SER M 42 " " THR 2 44 " - " LYS M 43 " " LYS 2 45 " - " THR M 44 " " GLU 2 46 " - " LYS M 45 " " GLY 2 47 " - " GLU M 46 " " VAL 2 48 " - " GLY M 47 " " VAL 2 49 " - " VAL M 48 " " HIS 2 50 " - " VAL M 49 " " GLY 2 51 " - " HIS M 50 " " VAL 2 52 " - " GLY M 51 " " ALA 2 53 " - " VAL M 52 " " THR 2 54 " - " ALA M 53 " " VAL 2 55 " - " THR M 54 " " ALA 2 56 " - " VAL M 55 " " GLU 2 57 " - " ALA M 56 " " LYS 2 58 " - " GLU M 57 " " LYS 2 60 " - " THR M 59 " " GLN 2 62 " - " GLU M 61 " " GLY 2 68 " - " GLY M 67 " " ALA 2 69 " - " GLY M 68 " " VAL 2 70 " - " ALA M 69 " " VAL 2 71 " - " VAL M 70 " " THR 2 72 " - " VAL M 71 " " GLY 2 73 " - " THR M 72 " " THR 2 81 " - " LYS M 80 " " VAL 2 82 " - " THR M 81 " " GLU 2 83 " - " VAL M 82 " " GLY 2 84 " - " GLU M 83 " " ALA 2 85 " - " GLY M 84 " " GLY 2 86 " - " ALA M 85 " " SER 2 87 " - " GLY M 86 " " ILE 2 88 " - " SER M 87 " " ALA 2 90 " - " ALA M 89 " " ALA 2 91 " - " ALA M 90 " " THR 2 92 " - " ALA M 91 " " GLY 2 93 " - " THR M 92 " " VAL 2 95 " - " PHE M 94 " " LYS 2 97 " - " LYS M 96 " " VAL 3 16 " - " VAL N 15 " " ALA 3 18 " - " ALA N 17 " " GLU 3 20 " - " ALA N 19 " " LYS 3 21 " - " GLU N 20 " " THR 3 22 " - " LYS N 21 " " LYS 3 23 " - " THR N 22 " " GLN 3 24 " - " LYS N 23 " " GLY 3 25 " - " GLN N 24 " " VAL 3 37 " - " GLY N 36 " " LEU 3 38 " - " VAL N 37 " " TYR 3 39 " - " LEU N 38 " " VAL 3 40 " - " TYR N 39 " " GLY 3 41 " - " VAL N 40 " " SER 3 42 " - " GLY N 41 " " LYS 3 43 " - " SER N 42 " " THR 3 44 " - " LYS N 43 " " LYS 3 45 " - " THR N 44 " " GLU 3 46 " - " LYS N 45 " " GLY 3 47 " - " GLU N 46 " " VAL 3 48 " - " GLY N 47 " " VAL 3 49 " - " VAL N 48 " " HIS 3 50 " - " VAL N 49 " " GLY 3 51 " - " HIS N 50 " " VAL 3 52 " - " GLY N 51 " " ALA 3 53 " - " VAL N 52 " " THR 3 54 " - " ALA N 53 " " VAL 3 55 " - " THR N 54 " " ALA 3 56 " - " VAL N 55 " " GLU 3 57 " - " ALA N 56 " " LYS 3 58 " - " GLU N 57 " " LYS 3 60 " - " THR N 59 " " GLN 3 62 " - " GLU N 61 " " GLY 3 68 " - " GLY N 67 " " ALA 3 69 " - " GLY N 68 " " VAL 3 70 " - " ALA N 69 " " VAL 3 71 " - " VAL N 70 " " THR 3 72 " - " VAL N 71 " " GLY 3 73 " - " THR N 72 " " THR 3 81 " - " LYS N 80 " " VAL 3 82 " - " THR N 81 " " GLU 3 83 " - " VAL N 82 " " GLY 3 84 " - " GLU N 83 " " ALA 3 85 " - " GLY N 84 " " GLY 3 86 " - " ALA N 85 " " SER 3 87 " - " GLY N 86 " " ILE 3 88 " - " SER N 87 " " ALA 3 90 " - " ALA N 89 " " ALA 3 91 " - " ALA N 90 " " THR 3 92 " - " ALA N 91 " " GLY 3 93 " - " THR N 92 " " VAL 3 95 " - " PHE N 94 " " LYS 3 97 " - " LYS N 96 " " UNK 4 6 " - " UNK O 5 " " UNK 5 6 " - " UNK P 5 " " VAL 6 15 " - " GLY e 14 " " VAL 6 16 " - " VAL e 15 " " ALA 6 17 " - " VAL e 16 " " ALA 6 18 " - " ALA e 17 " " ALA 6 19 " - " ALA e 18 " " LYS 6 21 " - " GLU e 20 " " LYS 6 23 " - " THR e 22 " " GLY 6 25 " - " GLN e 24 " " SER 6 42 " - " GLY e 41 " " VAL 6 48 " - " GLY A 47 " " HIS 6 50 " - " VAL e 49 " " THR 6 59 " - " LYS e 58 " " LYS 6 60 " - " THR e 59 " " GLU 6 61 " - " LYS e 60 " " GLN 6 62 " - " GLU e 61 " " VAL 6 63 " - " GLN e 62 " " THR 6 64 " - " VAL e 63 " " ASN 6 65 " - " THR e 64 " " VAL 6 66 " - " ASN e 65 " " GLY 6 67 " - " VAL e 66 " " ALA 6 69 " - " GLY e 68 " " VAL 6 71 " - " VAL e 70 " " GLY 6 73 " - " THR e 72 " " VAL 6 74 " - " GLY e 73 " " THR 6 75 " - " VAL e 74 " " ALA 6 76 " - " THR e 75 " " VAL 6 77 " - " ALA e 76 " " ALA 6 78 " - " VAL e 77 " " GLN 6 79 " - " ALA e 78 " " LYS 6 80 " - " GLN e 79 " " GLU 6 83 " - " VAL e 82 " " ALA 6 85 " - " GLY A 84 " " SER 6 87 " - " GLY e 86 " " ALA 6 89 " - " ILE e 88 " " PHE 6 94 " - " GLY A 93 " " VAL 6 95 " - " PHE A 94 " " LYS 6 96 " - " VAL e 95 " " LYS 6 97 " - " LYS A 96 " " ASP 6 98 " - " LYS e 97 " " GLN 6 99 " - " ASP e 98 " " LEU 6 100 " - " GLN e 99 " " VAL 7 15 " - " GLY f 14 " " VAL 7 16 " - " VAL f 15 " " ALA 7 17 " - " VAL f 16 " " ALA 7 18 " - " ALA f 17 " " ALA 7 19 " - " ALA f 18 " " LYS 7 21 " - " GLU f 20 " " LYS 7 23 " - " THR f 22 " " GLY 7 25 " - " GLN f 24 " " SER 7 42 " - " GLY f 41 " " VAL 7 48 " - " GLY C 47 " " HIS 7 50 " - " VAL f 49 " " THR 7 59 " - " LYS f 58 " " LYS 7 60 " - " THR f 59 " " GLU 7 61 " - " LYS f 60 " " GLN 7 62 " - " GLU f 61 " " VAL 7 63 " - " GLN f 62 " " THR 7 64 " - " VAL f 63 " " ASN 7 65 " - " THR f 64 " " VAL 7 66 " - " ASN f 65 " " GLY 7 67 " - " VAL f 66 " " ALA 7 69 " - " GLY f 68 " " VAL 7 71 " - " VAL f 70 " " GLY 7 73 " - " THR f 72 " " VAL 7 74 " - " GLY f 73 " " THR 7 75 " - " VAL f 74 " " ALA 7 76 " - " THR f 75 " " VAL 7 77 " - " ALA f 76 " " ALA 7 78 " - " VAL f 77 " " GLN 7 79 " - " ALA f 78 " " LYS 7 80 " - " GLN f 79 " " GLU 7 83 " - " VAL f 82 " " ALA 7 85 " - " GLY C 84 " " SER 7 87 " - " GLY f 86 " " ALA 7 89 " - " ILE f 88 " " PHE 7 94 " - " GLY C 93 " " VAL 7 95 " - " PHE C 94 " " LYS 7 96 " - " VAL f 95 " " LYS 7 97 " - " LYS C 96 " " ASP 7 98 " - " LYS f 97 " " GLN 7 99 " - " ASP f 98 " " LEU 7 100 " - " GLN f 99 " " UNK 8 2 " - " UNK g 1 " " UNK 8 3 " - " UNK g 2 " " UNK 8 4 " - " UNK g 3 " " UNK 8 5 " - " UNK g 4 " " UNK 8 6 " - " UNK B 5 " " UNK 8 7 " - " UNK g 6 " " UNK 8 8 " - " UNK g 7 " " UNK 8 9 " - " UNK B 8 " " UNK 9 2 " - " UNK h 1 " " UNK 9 3 " - " UNK h 2 " " UNK 9 4 " - " UNK h 3 " " UNK 9 5 " - " UNK h 4 " " UNK 9 6 " - " UNK D 5 " " UNK 9 7 " - " UNK D 6 " " UNK 9 8 " - " UNK h 7 " " UNK 9 9 " - " UNK D 8 " " GLU A 20 " - " ALA 6 19 " " THR A 22 " - " LYS e 21 " " GLN A 24 " - " LYS e 23 " " LYS A 43 " - " SER e 42 " " VAL A 48 " - " GLY e 47 " " GLY A 68 " - " GLY e 67 " " THR A 81 " - " LYS e 80 " " VAL A 82 " - " THR 6 81 " " ALA A 85 " - " GLY e 84 " " PHE A 94 " - " GLY e 93 " " VAL A 95 " - " PHE e 94 " " LYS A 97 " - " LYS e 96 " " UNK B 6 " - " UNK g 5 " " UNK B 9 " - " UNK g 8 " " GLU C 20 " - " ALA 7 19 " " THR C 22 " - " LYS f 21 " " GLN C 24 " - " LYS f 23 " " LYS C 43 " - " SER f 42 " " VAL C 48 " - " GLY f 47 " " GLY C 68 " - " GLY f 67 " " THR C 81 " - " LYS f 80 " " VAL C 82 " - " THR 7 81 " " ALA C 85 " - " GLY f 84 " " PHE C 94 " - " GLY f 93 " " VAL C 95 " - " PHE f 94 " " LYS C 97 " - " LYS f 96 " " UNK D 6 " - " UNK h 5 " " UNK D 7 " - " UNK h 6 " " UNK D 9 " - " UNK h 8 " " GLU E 20 " - " ALA Y 19 " " THR E 22 " - " LYS U 21 " " LYS E 23 " - " THR Y 22 " " GLN E 24 " - " LYS U 23 " " GLY E 25 " - " GLN Y 24 " " VAL E 37 " - " GLY Y 36 " " LEU E 38 " - " VAL U 37 " " TYR E 39 " - " LEU U 38 " " VAL E 40 " - " TYR U 39 " " GLY E 41 " - " VAL U 40 " " SER E 42 " - " GLY Y 41 " " LYS E 43 " - " SER U 42 " " THR E 44 " - " LYS U 43 " " LYS E 45 " - " THR U 44 " " GLU E 46 " - " LYS U 45 " " GLY E 47 " - " GLU U 46 " " VAL E 49 " - " VAL U 48 " " HIS E 50 " - " VAL Y 49 " " GLY E 51 " - " HIS U 50 " " VAL E 52 " - " GLY U 51 " " ALA E 53 " - " VAL U 52 " " THR E 54 " - " ALA U 53 " " VAL E 55 " - " THR U 54 " " ALA E 56 " - " VAL U 55 " " GLU E 57 " - " ALA U 56 " " LYS E 58 " - " GLU U 57 " " LYS E 60 " - " THR Y 59 " " GLN E 62 " - " GLU Y 61 " " ALA E 69 " - " GLY Y 68 " " VAL E 70 " - " ALA U 69 " " VAL E 71 " - " VAL Y 70 " " THR E 72 " - " VAL U 71 " " GLY E 73 " - " THR Y 72 " " THR E 81 " - " LYS U 80 " " VAL E 82 " - " THR Y 81 " " GLY E 84 " - " GLU Y 83 " " GLY E 86 " - " ALA U 85 " " SER E 87 " - " GLY Y 86 " " ILE E 88 " - " SER U 87 " " ALA E 90 " - " ALA U 89 " " ALA E 91 " - " ALA U 90 " " THR E 92 " - " ALA U 91 " " GLY E 93 " - " THR U 92 " " GLU F 20 " - " ALA Z 19 " " THR F 22 " - " LYS V 21 " " LYS F 23 " - " THR Z 22 " " GLN F 24 " - " LYS V 23 " " GLY F 25 " - " GLN Z 24 " " VAL F 37 " - " GLY Z 36 " " LEU F 38 " - " VAL V 37 " " TYR F 39 " - " LEU V 38 " " VAL F 40 " - " TYR V 39 " " GLY F 41 " - " VAL V 40 " " SER F 42 " - " GLY Z 41 " " LYS F 43 " - " SER V 42 " " THR F 44 " - " LYS V 43 " " LYS F 45 " - " THR V 44 " " GLU F 46 " - " LYS V 45 " " GLY F 47 " - " GLU V 46 " " VAL F 49 " - " VAL V 48 " " HIS F 50 " - " VAL Z 49 " " GLY F 51 " - " HIS V 50 " " VAL F 52 " - " GLY V 51 " " ALA F 53 " - " VAL V 52 " " THR F 54 " - " ALA V 53 " " VAL F 55 " - " THR V 54 " " ALA F 56 " - " VAL V 55 " " GLU F 57 " - " ALA V 56 " " LYS F 58 " - " GLU V 57 " " LYS F 60 " - " THR Z 59 " " GLN F 62 " - " GLU Z 61 " " ALA F 69 " - " GLY Z 68 " " VAL F 70 " - " ALA V 69 " " VAL F 71 " - " VAL Z 70 " " THR F 72 " - " VAL V 71 " " GLY F 73 " - " THR Z 72 " " THR F 81 " - " LYS V 80 " " VAL F 82 " - " THR Z 81 " " GLY F 84 " - " GLU Z 83 " " GLY F 86 " - " ALA V 85 " " SER F 87 " - " GLY Z 86 " " ILE F 88 " - " SER V 87 " " ALA F 90 " - " ALA V 89 " " ALA F 91 " - " ALA V 90 " " THR F 92 " - " ALA V 91 " " GLY F 93 " - " THR V 92 " " VAL I 15 " - " GLY q 14 " " VAL I 16 " - " VAL q 15 " " ALA I 17 " - " VAL q 16 " " ALA I 18 " - " ALA q 17 " " ALA I 19 " - " ALA q 18 " " LYS I 21 " - " GLU q 20 " " LYS I 23 " - " THR q 22 " " GLY I 25 " - " GLN q 24 " " SER I 42 " - " GLY q 41 " " VAL I 48 " - " GLY a 47 " " HIS I 50 " - " VAL q 49 " " THR I 59 " - " LYS q 58 " " LYS I 60 " - " THR q 59 " " GLU I 61 " - " LYS q 60 " " GLN I 62 " - " GLU q 61 " " VAL I 63 " - " GLN q 62 " " THR I 64 " - " VAL q 63 " " ASN I 65 " - " THR q 64 " " VAL I 66 " - " ASN q 65 " " GLY I 67 " - " VAL q 66 " " ALA I 69 " - " GLY q 68 " " VAL I 71 " - " VAL q 70 " " GLY I 73 " - " THR q 72 " " VAL I 74 " - " GLY q 73 " " THR I 75 " - " VAL q 74 " " ALA I 76 " - " THR q 75 " " VAL I 77 " - " ALA q 76 " " ALA I 78 " - " VAL q 77 " " GLN I 79 " - " ALA q 78 " " LYS I 80 " - " GLN q 79 " " GLU I 83 " - " VAL q 82 " " ALA I 85 " - " GLY a 84 " " SER I 87 " - " GLY q 86 " " ALA I 89 " - " ILE q 88 " " PHE I 94 " - " GLY a 93 " " VAL I 95 " - " PHE a 94 " " LYS I 96 " - " VAL q 95 " " LYS I 97 " - " LYS a 96 " " ASP I 98 " - " LYS q 97 " " GLN I 99 " - " ASP q 98 " " LEU I 100 " - " GLN q 99 " " VAL J 15 " - " GLY r 14 " " VAL J 16 " - " VAL r 15 " " ALA J 17 " - " VAL r 16 " " ALA J 18 " - " ALA r 17 " " ALA J 19 " - " ALA r 18 " " LYS J 21 " - " GLU r 20 " " LYS J 23 " - " THR r 22 " " GLY J 25 " - " GLN r 24 " " SER J 42 " - " GLY r 41 " " VAL J 48 " - " GLY b 47 " " HIS J 50 " - " VAL r 49 " " THR J 59 " - " LYS r 58 " " LYS J 60 " - " THR r 59 " " GLU J 61 " - " LYS r 60 " " GLN J 62 " - " GLU r 61 " " VAL J 63 " - " GLN r 62 " " THR J 64 " - " VAL r 63 " " ASN J 65 " - " THR r 64 " " VAL J 66 " - " ASN r 65 " " GLY J 67 " - " VAL r 66 " " ALA J 69 " - " GLY r 68 " " VAL J 71 " - " VAL r 70 " " GLY J 73 " - " THR r 72 " " VAL J 74 " - " GLY r 73 " " THR J 75 " - " VAL r 74 " " ALA J 76 " - " THR r 75 " " VAL J 77 " - " ALA r 76 " " ALA J 78 " - " VAL r 77 " " GLN J 79 " - " ALA r 78 " " LYS J 80 " - " GLN r 79 " " GLU J 83 " - " VAL r 82 " " ALA J 85 " - " GLY b 84 " " SER J 87 " - " GLY r 86 " " ALA J 89 " - " ILE r 88 " " PHE J 94 " - " GLY b 93 " " VAL J 95 " - " PHE b 94 " " LYS J 96 " - " VAL r 95 " " LYS J 97 " - " LYS b 96 " " ASP J 98 " - " LYS r 97 " " GLN J 99 " - " ASP r 98 " " LEU J 100 " - " GLN r 99 " " UNK K 2 " - " UNK s 1 " " UNK K 3 " - " UNK s 2 " " UNK K 4 " - " UNK s 3 " " UNK K 5 " - " UNK s 4 " " UNK K 6 " - " UNK c 5 " " UNK K 7 " - " UNK s 6 " " UNK K 8 " - " UNK s 7 " " UNK K 9 " - " UNK c 8 " " UNK L 2 " - " UNK t 1 " " UNK L 3 " - " UNK t 2 " " UNK L 4 " - " UNK t 3 " " UNK L 5 " - " UNK t 4 " " UNK L 6 " - " UNK d 5 " " UNK L 7 " - " UNK d 6 " " UNK L 8 " - " UNK t 7 " " UNK L 9 " - " UNK d 8 " " VAL M 15 " - " GLY 2 14 " " VAL M 16 " - " VAL 2 15 " " ALA M 17 " - " VAL 2 16 " " ALA M 18 " - " ALA 2 17 " " ALA M 19 " - " ALA 2 18 " " GLU M 20 " - " ALA 2 19 " " LYS M 21 " - " GLU 2 20 " " THR M 22 " - " LYS 2 21 " " LYS M 23 " - " THR 2 22 " " GLN M 24 " - " LYS 2 23 " " GLY M 25 " - " GLN 2 24 " " SER M 42 " - " GLY 2 41 " " LYS M 43 " - " SER 2 42 " " VAL M 48 " - " GLY 2 47 " " HIS M 50 " - " VAL 2 49 " " THR M 59 " - " LYS 2 58 " " LYS M 60 " - " THR 2 59 " " GLU M 61 " - " LYS 2 60 " " GLN M 62 " - " GLU 2 61 " " VAL M 63 " - " GLN 2 62 " " THR M 64 " - " VAL 2 63 " " ASN M 65 " - " THR 2 64 " " VAL M 66 " - " ASN 2 65 " " GLY M 67 " - " VAL 2 66 " " GLY M 68 " - " GLY 2 67 " " ALA M 69 " - " GLY 2 68 " " VAL M 71 " - " VAL 2 70 " " GLY M 73 " - " THR 2 72 " " VAL M 74 " - " GLY 2 73 " " THR M 75 " - " VAL 2 74 " " ALA M 76 " - " THR 2 75 " " VAL M 77 " - " ALA 2 76 " " ALA M 78 " - " VAL 2 77 " " GLN M 79 " - " ALA 2 78 " " LYS M 80 " - " GLN 2 79 " " THR M 81 " - " LYS 2 80 " " GLU M 83 " - " VAL 2 82 " " ALA M 85 " - " GLY 2 84 " " SER M 87 " - " GLY 2 86 " " ALA M 89 " - " ILE 2 88 " " PHE M 94 " - " GLY 2 93 " " VAL M 95 " - " PHE 2 94 " " LYS M 96 " - " VAL 2 95 " " LYS M 97 " - " LYS 2 96 " " ASP M 98 " - " LYS 2 97 " " GLN M 99 " - " ASP 2 98 " " LEU M 100 " - " GLN 2 99 " " VAL N 15 " - " GLY 3 14 " " VAL N 16 " - " VAL 3 15 " " ALA N 17 " - " VAL 3 16 " " ALA N 18 " - " ALA 3 17 " " ALA N 19 " - " ALA 3 18 " " GLU N 20 " - " ALA 3 19 " " LYS N 21 " - " GLU 3 20 " " THR N 22 " - " LYS 3 21 " " LYS N 23 " - " THR 3 22 " " GLN N 24 " - " LYS 3 23 " " GLY N 25 " - " GLN 3 24 " " SER N 42 " - " GLY 3 41 " " LYS N 43 " - " SER 3 42 " " VAL N 48 " - " GLY 3 47 " " HIS N 50 " - " VAL 3 49 " " THR N 59 " - " LYS 3 58 " " LYS N 60 " - " THR 3 59 " " GLU N 61 " - " LYS 3 60 " " GLN N 62 " - " GLU 3 61 " " VAL N 63 " - " GLN 3 62 " " THR N 64 " - " VAL 3 63 " " ASN N 65 " - " THR 3 64 " " VAL N 66 " - " ASN 3 65 " " GLY N 67 " - " VAL 3 66 " " GLY N 68 " - " GLY 3 67 " " ALA N 69 " - " GLY 3 68 " " VAL N 71 " - " VAL 3 70 " " GLY N 73 " - " THR 3 72 " " VAL N 74 " - " GLY 3 73 " " THR N 75 " - " VAL 3 74 " " ALA N 76 " - " THR 3 75 " " VAL N 77 " - " ALA 3 76 " " ALA N 78 " - " VAL 3 77 " " GLN N 79 " - " ALA 3 78 " " LYS N 80 " - " GLN 3 79 " " THR N 81 " - " LYS 3 80 " " GLU N 83 " - " VAL 3 82 " " ALA N 85 " - " GLY 3 84 " " SER N 87 " - " GLY 3 86 " " ALA N 89 " - " ILE 3 88 " " PHE N 94 " - " GLY 3 93 " " VAL N 95 " - " PHE 3 94 " " LYS N 96 " - " VAL 3 95 " " LYS N 97 " - " LYS 3 96 " " ASP N 98 " - " LYS 3 97 " " GLN N 99 " - " ASP 3 98 " " LEU N 100 " - " GLN 3 99 " " UNK O 2 " - " UNK 4 1 " " UNK O 3 " - " UNK 4 2 " " UNK O 4 " - " UNK 4 3 " " UNK O 5 " - " UNK 4 4 " " UNK O 6 " - " UNK 4 5 " " UNK O 7 " - " UNK 4 6 " " UNK O 8 " - " UNK 4 7 " " UNK O 9 " - " UNK 4 8 " " UNK P 2 " - " UNK 5 1 " " UNK P 3 " - " UNK 5 2 " " UNK P 4 " - " UNK 5 3 " " UNK P 5 " - " UNK 5 4 " " UNK P 6 " - " UNK 5 5 " " UNK P 7 " - " UNK 5 6 " " UNK P 8 " - " UNK 5 7 " " UNK P 9 " - " UNK 5 8 " " VAL U 15 " - " GLY E 14 " " VAL U 16 " - " VAL E 15 " " ALA U 17 " - " VAL E 16 " " ALA U 18 " - " ALA E 17 " " ALA U 19 " - " ALA E 18 " " LYS U 21 " - " GLU E 20 " " LYS U 23 " - " THR E 22 " " GLY U 25 " - " GLN E 24 " " SER U 42 " - " GLY E 41 " " VAL U 48 " - " GLY Y 47 " " HIS U 50 " - " VAL E 49 " " THR U 59 " - " LYS E 58 " " LYS U 60 " - " THR E 59 " " GLU U 61 " - " LYS E 60 " " GLN U 62 " - " GLU E 61 " " VAL U 63 " - " GLN E 62 " " THR U 64 " - " VAL E 63 " " ASN U 65 " - " THR E 64 " " VAL U 66 " - " ASN E 65 " " GLY U 67 " - " VAL E 66 " " ALA U 69 " - " GLY E 68 " " VAL U 71 " - " VAL E 70 " " GLY U 73 " - " THR E 72 " " VAL U 74 " - " GLY E 73 " " THR U 75 " - " VAL E 74 " " ALA U 76 " - " THR E 75 " " VAL U 77 " - " ALA E 76 " " ALA U 78 " - " VAL E 77 " " GLN U 79 " - " ALA E 78 " " LYS U 80 " - " GLN E 79 " " GLU U 83 " - " VAL E 82 " " ALA U 85 " - " GLY Y 84 " " SER U 87 " - " GLY E 86 " " ALA U 89 " - " ILE E 88 " " PHE U 94 " - " GLY Y 93 " " VAL U 95 " - " PHE Y 94 " " LYS U 96 " - " VAL E 95 " " LYS U 97 " - " LYS Y 96 " " ASP U 98 " - " LYS E 97 " " GLN U 99 " - " ASP E 98 " " LEU U 100 " - " GLN E 99 " " VAL V 15 " - " GLY F 14 " " VAL V 16 " - " VAL F 15 " " ALA V 17 " - " VAL F 16 " " ALA V 18 " - " ALA F 17 " " ALA V 19 " - " ALA F 18 " " LYS V 21 " - " GLU F 20 " " LYS V 23 " - " THR F 22 " " GLY V 25 " - " GLN F 24 " " SER V 42 " - " GLY F 41 " " VAL V 48 " - " GLY Z 47 " " HIS V 50 " - " VAL F 49 " " THR V 59 " - " LYS F 58 " " LYS V 60 " - " THR F 59 " " GLU V 61 " - " LYS F 60 " " GLN V 62 " - " GLU F 61 " " VAL V 63 " - " GLN F 62 " " THR V 64 " - " VAL F 63 " " ASN V 65 " - " THR F 64 " " VAL V 66 " - " ASN F 65 " " GLY V 67 " - " VAL F 66 " " ALA V 69 " - " GLY F 68 " " VAL V 71 " - " VAL F 70 " " GLY V 73 " - " THR F 72 " " VAL V 74 " - " GLY Z 73 " " THR V 75 " - " VAL F 74 " " ALA V 76 " - " THR F 75 " " VAL V 77 " - " ALA F 76 " " ALA V 78 " - " VAL F 77 " " GLN V 79 " - " ALA F 78 " " LYS V 80 " - " GLN F 79 " " GLU V 83 " - " VAL F 82 " " ALA V 85 " - " GLY Z 84 " " SER V 87 " - " GLY F 86 " " ALA V 89 " - " ILE F 88 " " PHE V 94 " - " GLY Z 93 " " VAL V 95 " - " PHE Z 94 " " LYS V 96 " - " VAL F 95 " " LYS V 97 " - " LYS Z 96 " " ASP V 98 " - " LYS F 97 " " GLN V 99 " - " ASP F 98 " " LEU V 100 " - " GLN F 99 " " UNK W 2 " - " UNK G 1 " " UNK W 3 " - " UNK G 2 " " UNK W 4 " - " UNK G 3 " " UNK W 5 " - " UNK G 4 " " UNK W 6 " - " UNK 0 5 " " UNK W 7 " - " UNK G 6 " " UNK W 8 " - " UNK G 7 " " UNK W 9 " - " UNK 0 8 " " UNK X 2 " - " UNK H 1 " " UNK X 3 " - " UNK H 2 " " UNK X 4 " - " UNK H 3 " " UNK X 5 " - " UNK H 4 " " UNK X 6 " - " UNK 1 5 " " UNK X 7 " - " UNK 1 6 " " UNK X 8 " - " UNK H 7 " " UNK X 9 " - " UNK 1 8 " " GLU Y 20 " - " ALA U 19 " " THR Y 22 " - " LYS E 21 " " GLN Y 24 " - " LYS E 23 " " LYS Y 43 " - " SER E 42 " " VAL Y 48 " - " GLY E 47 " " GLY Y 68 " - " GLY E 67 " " THR Y 81 " - " LYS E 80 " " VAL Y 82 " - " THR U 81 " " ALA Y 85 " - " GLY E 84 " " PHE Y 94 " - " GLY E 93 " " VAL Y 95 " - " PHE E 94 " " LYS Y 97 " - " LYS E 96 " " GLU Z 20 " - " ALA V 19 " " THR Z 22 " - " LYS F 21 " " GLN Z 24 " - " LYS F 23 " " LYS Z 43 " - " SER F 42 " " VAL Z 48 " - " GLY F 47 " " GLY Z 68 " - " GLY F 67 " " VAL Z 74 " - " GLY F 73 " " THR Z 81 " - " LYS F 80 " " VAL Z 82 " - " THR V 81 " " ALA Z 85 " - " GLY F 84 " " PHE Z 94 " - " GLY F 93 " " VAL Z 95 " - " PHE F 94 " " LYS Z 97 " - " LYS F 96 " " GLU a 20 " - " ALA I 19 " " THR a 22 " - " LYS q 21 " " GLN a 24 " - " LYS q 23 " " LYS a 43 " - " SER q 42 " " VAL a 48 " - " GLY q 47 " " GLY a 68 " - " GLY q 67 " " THR a 81 " - " LYS q 80 " " VAL a 82 " - " THR I 81 " " ALA a 85 " - " GLY q 84 " " PHE a 94 " - " GLY q 93 " " VAL a 95 " - " PHE q 94 " " LYS a 97 " - " LYS q 96 " " GLU b 20 " - " ALA J 19 " " THR b 22 " - " LYS r 21 " " GLN b 24 " - " LYS r 23 " " LYS b 43 " - " SER r 42 " " VAL b 48 " - " GLY r 47 " " GLY b 68 " - " GLY r 67 " " THR b 81 " - " LYS r 80 " " VAL b 82 " - " THR J 81 " " ALA b 85 " - " GLY r 84 " " PHE b 94 " - " GLY r 93 " " VAL b 95 " - " PHE r 94 " " LYS b 97 " - " LYS r 96 " " UNK c 6 " - " UNK s 5 " " UNK c 9 " - " UNK s 8 " " UNK d 6 " - " UNK t 5 " " UNK d 7 " - " UNK t 6 " " UNK d 9 " - " UNK t 8 " " GLU e 20 " - " ALA A 19 " " THR e 22 " - " LYS 6 21 " " LYS e 23 " - " THR A 22 " " GLN e 24 " - " LYS 6 23 " " GLY e 25 " - " GLN A 24 " " VAL e 37 " - " GLY A 36 " " LEU e 38 " - " VAL 6 37 " " TYR e 39 " - " LEU 6 38 " " VAL e 40 " - " TYR 6 39 " " GLY e 41 " - " VAL 6 40 " " SER e 42 " - " GLY A 41 " " LYS e 43 " - " SER 6 42 " " THR e 44 " - " LYS 6 43 " " LYS e 45 " - " THR 6 44 " " GLU e 46 " - " LYS 6 45 " " GLY e 47 " - " GLU 6 46 " " VAL e 49 " - " VAL 6 48 " " HIS e 50 " - " VAL A 49 " " GLY e 51 " - " HIS 6 50 " " VAL e 52 " - " GLY 6 51 " " ALA e 53 " - " VAL 6 52 " " THR e 54 " - " ALA 6 53 " " VAL e 55 " - " THR 6 54 " " ALA e 56 " - " VAL 6 55 " " GLU e 57 " - " ALA 6 56 " " LYS e 58 " - " GLU 6 57 " " LYS e 60 " - " THR A 59 " " GLN e 62 " - " GLU A 61 " " ALA e 69 " - " GLY A 68 " " VAL e 70 " - " ALA 6 69 " " VAL e 71 " - " VAL A 70 " " THR e 72 " - " VAL 6 71 " " GLY e 73 " - " THR A 72 " " THR e 81 " - " LYS 6 80 " " VAL e 82 " - " THR A 81 " " GLY e 84 " - " GLU A 83 " " GLY e 86 " - " ALA 6 85 " " SER e 87 " - " GLY A 86 " " ILE e 88 " - " SER 6 87 " " ALA e 90 " - " ALA 6 89 " " ALA e 91 " - " ALA 6 90 " " THR e 92 " - " ALA 6 91 " " GLY e 93 " - " THR 6 92 " " GLU f 20 " - " ALA C 19 " " THR f 22 " - " LYS 7 21 " " LYS f 23 " - " THR C 22 " " GLN f 24 " - " LYS 7 23 " " GLY f 25 " - " GLN C 24 " " VAL f 37 " - " GLY C 36 " " LEU f 38 " - " VAL 7 37 " " TYR f 39 " - " LEU 7 38 " " VAL f 40 " - " TYR 7 39 " " GLY f 41 " - " VAL 7 40 " " SER f 42 " - " GLY C 41 " " LYS f 43 " - " SER 7 42 " " THR f 44 " - " LYS 7 43 " " LYS f 45 " - " THR 7 44 " " GLU f 46 " - " LYS 7 45 " " GLY f 47 " - " GLU 7 46 " " VAL f 49 " - " VAL 7 48 " " HIS f 50 " - " VAL C 49 " " GLY f 51 " - " HIS 7 50 " " VAL f 52 " - " GLY 7 51 " " ALA f 53 " - " VAL 7 52 " " THR f 54 " - " ALA 7 53 " " VAL f 55 " - " THR 7 54 " " ALA f 56 " - " VAL 7 55 " " GLU f 57 " - " ALA 7 56 " " LYS f 58 " - " GLU 7 57 " " LYS f 60 " - " THR C 59 " " GLN f 62 " - " GLU C 61 " " ALA f 69 " - " GLY C 68 " " VAL f 70 " - " ALA 7 69 " " VAL f 71 " - " VAL C 70 " " THR f 72 " - " VAL 7 71 " " GLY f 73 " - " THR C 72 " " THR f 81 " - " LYS 7 80 " " VAL f 82 " - " THR C 81 " " GLY f 84 " - " GLU C 83 " " GLY f 86 " - " ALA 7 85 " " SER f 87 " - " GLY C 86 " " ILE f 88 " - " SER 7 87 " " ALA f 90 " - " ALA 7 89 " " ALA f 91 " - " ALA 7 90 " " THR f 92 " - " ALA 7 91 " " GLY f 93 " - " THR 7 92 " " VAL i 15 " - " GLY m 14 " " VAL i 16 " - " VAL m 15 " " ALA i 17 " - " VAL m 16 " " ALA i 18 " - " ALA m 17 " " ALA i 19 " - " ALA m 18 " " GLU i 20 " - " ALA m 19 " " LYS i 21 " - " GLU m 20 " " THR i 22 " - " LYS m 21 " " LYS i 23 " - " THR m 22 " " GLN i 24 " - " LYS m 23 " " GLY i 25 " - " GLN m 24 " " SER i 42 " - " GLY m 41 " " LYS i 43 " - " SER m 42 " " VAL i 48 " - " GLY m 47 " " HIS i 50 " - " VAL m 49 " " THR i 59 " - " LYS m 58 " " LYS i 60 " - " THR m 59 " " GLU i 61 " - " LYS m 60 " " GLN i 62 " - " GLU m 61 " " VAL i 63 " - " GLN m 62 " " THR i 64 " - " VAL m 63 " " ASN i 65 " - " THR m 64 " " VAL i 66 " - " ASN m 65 " " GLY i 67 " - " VAL m 66 " " GLY i 68 " - " GLY m 67 " " ALA i 69 " - " GLY m 68 " " VAL i 71 " - " VAL m 70 " " GLY i 73 " - " THR m 72 " " VAL i 74 " - " GLY m 73 " " THR i 75 " - " VAL m 74 " " ALA i 76 " - " THR m 75 " " VAL i 77 " - " ALA m 76 " " ALA i 78 " - " VAL m 77 " " GLN i 79 " - " ALA m 78 " " LYS i 80 " - " GLN m 79 " " THR i 81 " - " LYS m 80 " " GLU i 83 " - " VAL m 82 " " ALA i 85 " - " GLY m 84 " " SER i 87 " - " GLY m 86 " " ALA i 89 " - " ILE m 88 " " PHE i 94 " - " GLY m 93 " " VAL i 95 " - " PHE m 94 " " LYS i 96 " - " VAL m 95 " " LYS i 97 " - " LYS m 96 " " ASP i 98 " - " LYS m 97 " " GLN i 99 " - " ASP m 98 " " LEU i 100 " - " GLN m 99 " " VAL j 15 " - " GLY n 14 " " VAL j 16 " - " VAL n 15 " " ALA j 17 " - " VAL n 16 " " ALA j 18 " - " ALA n 17 " " ALA j 19 " - " ALA n 18 " " GLU j 20 " - " ALA n 19 " " LYS j 21 " - " GLU n 20 " " THR j 22 " - " LYS n 21 " " LYS j 23 " - " THR n 22 " " GLN j 24 " - " LYS n 23 " " GLY j 25 " - " GLN n 24 " " SER j 42 " - " GLY n 41 " " LYS j 43 " - " SER n 42 " " VAL j 48 " - " GLY n 47 " " HIS j 50 " - " VAL n 49 " " THR j 59 " - " LYS n 58 " " LYS j 60 " - " THR n 59 " " GLU j 61 " - " LYS n 60 " " GLN j 62 " - " GLU n 61 " " VAL j 63 " - " GLN n 62 " " THR j 64 " - " VAL n 63 " " ASN j 65 " - " THR n 64 " " VAL j 66 " - " ASN n 65 " " GLY j 67 " - " VAL n 66 " " GLY j 68 " - " GLY n 67 " " ALA j 69 " - " GLY n 68 " " VAL j 71 " - " VAL n 70 " " GLY j 73 " - " THR n 72 " " VAL j 74 " - " GLY n 73 " " THR j 75 " - " VAL n 74 " " ALA j 76 " - " THR n 75 " " VAL j 77 " - " ALA n 76 " " ALA j 78 " - " VAL n 77 " " GLN j 79 " - " ALA n 78 " " LYS j 80 " - " GLN n 79 " " THR j 81 " - " LYS n 80 " " GLU j 83 " - " VAL n 82 " " ALA j 85 " - " GLY n 84 " " SER j 87 " - " GLY n 86 " " ALA j 89 " - " ILE n 88 " " PHE j 94 " - " GLY n 93 " " VAL j 95 " - " PHE n 94 " " LYS j 96 " - " VAL n 95 " " LYS j 97 " - " LYS n 96 " " ASP j 98 " - " LYS n 97 " " GLN j 99 " - " ASP n 98 " " LEU j 100 " - " GLN n 99 " " UNK k 2 " - " UNK o 1 " " UNK k 3 " - " UNK o 2 " " UNK k 4 " - " UNK o 3 " " UNK k 5 " - " UNK o 4 " " UNK k 6 " - " UNK o 5 " " UNK k 7 " - " UNK o 6 " " UNK k 8 " - " UNK o 7 " " UNK k 9 " - " UNK o 8 " " UNK l 2 " - " UNK p 1 " " UNK l 3 " - " UNK p 2 " " UNK l 4 " - " UNK p 3 " " UNK l 5 " - " UNK p 4 " " UNK l 6 " - " UNK p 5 " " UNK l 7 " - " UNK p 6 " " UNK l 8 " - " UNK p 7 " " UNK l 9 " - " UNK p 8 " " VAL m 16 " - " VAL i 15 " " ALA m 18 " - " ALA i 17 " " GLU m 20 " - " ALA i 19 " " LYS m 21 " - " GLU i 20 " " THR m 22 " - " LYS i 21 " " LYS m 23 " - " THR i 22 " " GLN m 24 " - " LYS i 23 " " GLY m 25 " - " GLN i 24 " " VAL m 37 " - " GLY i 36 " " LEU m 38 " - " VAL i 37 " " TYR m 39 " - " LEU i 38 " " VAL m 40 " - " TYR i 39 " " GLY m 41 " - " VAL i 40 " " SER m 42 " - " GLY i 41 " " LYS m 43 " - " SER i 42 " " THR m 44 " - " LYS i 43 " " LYS m 45 " - " THR i 44 " " GLU m 46 " - " LYS i 45 " " GLY m 47 " - " GLU i 46 " " VAL m 48 " - " GLY i 47 " " VAL m 49 " - " VAL i 48 " " HIS m 50 " - " VAL i 49 " " GLY m 51 " - " HIS i 50 " " VAL m 52 " - " GLY i 51 " " ALA m 53 " - " VAL i 52 " " THR m 54 " - " ALA i 53 " " VAL m 55 " - " THR i 54 " " ALA m 56 " - " VAL i 55 " " GLU m 57 " - " ALA i 56 " " LYS m 58 " - " GLU i 57 " " LYS m 60 " - " THR i 59 " " GLN m 62 " - " GLU i 61 " " GLY m 68 " - " GLY i 67 " " ALA m 69 " - " GLY i 68 " " VAL m 70 " - " ALA i 69 " " VAL m 71 " - " VAL i 70 " " THR m 72 " - " VAL i 71 " " GLY m 73 " - " THR i 72 " " THR m 81 " - " LYS i 80 " " VAL m 82 " - " THR i 81 " " GLU m 83 " - " VAL i 82 " " GLY m 84 " - " GLU i 83 " " ALA m 85 " - " GLY i 84 " " GLY m 86 " - " ALA i 85 " " SER m 87 " - " GLY i 86 " " ILE m 88 " - " SER i 87 " " ALA m 90 " - " ALA i 89 " " ALA m 91 " - " ALA i 90 " " THR m 92 " - " ALA i 91 " " GLY m 93 " - " THR i 92 " " VAL m 95 " - " PHE i 94 " " LYS m 97 " - " LYS i 96 " " VAL n 16 " - " VAL j 15 " " ALA n 18 " - " ALA j 17 " " GLU n 20 " - " ALA j 19 " " LYS n 21 " - " GLU j 20 " " THR n 22 " - " LYS j 21 " " LYS n 23 " - " THR j 22 " " GLN n 24 " - " LYS j 23 " " GLY n 25 " - " GLN j 24 " " VAL n 37 " - " GLY j 36 " " LEU n 38 " - " VAL j 37 " " TYR n 39 " - " LEU j 38 " " VAL n 40 " - " TYR j 39 " " GLY n 41 " - " VAL j 40 " " SER n 42 " - " GLY j 41 " " LYS n 43 " - " SER j 42 " " THR n 44 " - " LYS j 43 " " LYS n 45 " - " THR j 44 " " GLU n 46 " - " LYS j 45 " " GLY n 47 " - " GLU j 46 " " VAL n 48 " - " GLY j 47 " " VAL n 49 " - " VAL j 48 " " HIS n 50 " - " VAL j 49 " " GLY n 51 " - " HIS j 50 " " VAL n 52 " - " GLY j 51 " " ALA n 53 " - " VAL j 52 " " THR n 54 " - " ALA j 53 " " VAL n 55 " - " THR j 54 " " ALA n 56 " - " VAL j 55 " " GLU n 57 " - " ALA j 56 " " LYS n 58 " - " GLU j 57 " " LYS n 60 " - " THR j 59 " " GLN n 62 " - " GLU j 61 " " GLY n 68 " - " GLY j 67 " " ALA n 69 " - " GLY j 68 " " VAL n 70 " - " ALA j 69 " " VAL n 71 " - " VAL j 70 " " THR n 72 " - " VAL j 71 " " GLY n 73 " - " THR j 72 " " THR n 81 " - " LYS j 80 " " VAL n 82 " - " THR j 81 " " GLU n 83 " - " VAL j 82 " " GLY n 84 " - " GLU j 83 " " ALA n 85 " - " GLY j 84 " " GLY n 86 " - " ALA j 85 " " SER n 87 " - " GLY j 86 " " ILE n 88 " - " SER j 87 " " ALA n 90 " - " ALA j 89 " " ALA n 91 " - " ALA j 90 " " THR n 92 " - " ALA j 91 " " GLY n 93 " - " THR j 92 " " VAL n 95 " - " PHE j 94 " " LYS n 97 " - " LYS j 96 " " UNK o 6 " - " UNK k 5 " " UNK p 6 " - " UNK l 5 " " GLU q 20 " - " ALA a 19 " " THR q 22 " - " LYS I 21 " " LYS q 23 " - " THR a 22 " " GLN q 24 " - " LYS I 23 " " GLY q 25 " - " GLN a 24 " " VAL q 37 " - " GLY a 36 " " LEU q 38 " - " VAL I 37 " " TYR q 39 " - " LEU I 38 " " VAL q 40 " - " TYR I 39 " " GLY q 41 " - " VAL I 40 " " SER q 42 " - " GLY a 41 " " LYS q 43 " - " SER I 42 " " THR q 44 " - " LYS I 43 " " LYS q 45 " - " THR I 44 " " GLU q 46 " - " LYS I 45 " " GLY q 47 " - " GLU I 46 " " VAL q 49 " - " VAL I 48 " " HIS q 50 " - " VAL a 49 " " GLY q 51 " - " HIS I 50 " " VAL q 52 " - " GLY I 51 " " ALA q 53 " - " VAL I 52 " " THR q 54 " - " ALA I 53 " " VAL q 55 " - " THR I 54 " " ALA q 56 " - " VAL I 55 " " GLU q 57 " - " ALA I 56 " " LYS q 58 " - " GLU I 57 " " LYS q 60 " - " THR a 59 " " GLN q 62 " - " GLU a 61 " " ALA q 69 " - " GLY a 68 " " VAL q 70 " - " ALA I 69 " " VAL q 71 " - " VAL a 70 " " THR q 72 " - " VAL I 71 " " GLY q 73 " - " THR a 72 " " THR q 81 " - " LYS I 80 " " VAL q 82 " - " THR a 81 " " GLY q 84 " - " GLU a 83 " " GLY q 86 " - " ALA I 85 " " SER q 87 " - " GLY a 86 " " ILE q 88 " - " SER I 87 " " ALA q 90 " - " ALA I 89 " " ALA q 91 " - " ALA I 90 " " THR q 92 " - " ALA I 91 " " GLY q 93 " - " THR I 92 " " GLU r 20 " - " ALA b 19 " " THR r 22 " - " LYS J 21 " " LYS r 23 " - " THR b 22 " " GLN r 24 " - " LYS J 23 " " GLY r 25 " - " GLN b 24 " " VAL r 37 " - " GLY b 36 " " LEU r 38 " - " VAL J 37 " " TYR r 39 " - " LEU J 38 " " VAL r 40 " - " TYR J 39 " " GLY r 41 " - " VAL J 40 " " SER r 42 " - " GLY b 41 " " LYS r 43 " - " SER J 42 " " THR r 44 " - " LYS J 43 " " LYS r 45 " - " THR J 44 " " GLU r 46 " - " LYS J 45 " " GLY r 47 " - " GLU J 46 " " VAL r 49 " - " VAL J 48 " " HIS r 50 " - " VAL b 49 " " GLY r 51 " - " HIS J 50 " " VAL r 52 " - " GLY J 51 " " ALA r 53 " - " VAL J 52 " " THR r 54 " - " ALA J 53 " " VAL r 55 " - " THR J 54 " " ALA r 56 " - " VAL J 55 " " GLU r 57 " - " ALA J 56 " " LYS r 58 " - " GLU J 57 " " LYS r 60 " - " THR b 59 " " GLN r 62 " - " GLU b 61 " " ALA r 69 " - " GLY b 68 " " VAL r 70 " - " ALA J 69 " " VAL r 71 " - " VAL b 70 " " THR r 72 " - " VAL J 71 " " GLY r 73 " - " THR b 72 " " THR r 81 " - " LYS J 80 " " VAL r 82 " - " THR b 81 " " GLY r 84 " - " GLU b 83 " " GLY r 86 " - " ALA J 85 " " SER r 87 " - " GLY b 86 " " ILE r 88 " - " SER J 87 " " ALA r 90 " - " ALA J 89 " " ALA r 91 " - " ALA J 90 " " THR r 92 " - " ALA J 91 " " GLY r 93 " - " THR J 92 " Time building additional restraints: 7.66 Conformation dependent library (CDL) restraints added in 893.4 milliseconds 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 8.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 3090 1.29 - 1.35: 2730 1.35 - 1.42: 450 1.42 - 1.48: 3088 1.48 - 1.55: 7892 Bond restraints: 17250 Sorted by residual: bond pdb=" CA ALA q 89 " pdb=" CB ALA q 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.50e+00 bond pdb=" CA ALA U 89 " pdb=" CB ALA U 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.48e+00 bond pdb=" CA ALA m 89 " pdb=" CB ALA m 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.46e+00 bond pdb=" CA ALA Y 89 " pdb=" CB ALA Y 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.43e+00 bond pdb=" CA ALA u 89 " pdb=" CB ALA u 89 " ideal model delta sigma weight residual 1.529 1.495 0.034 1.62e-02 3.81e+03 4.42e+00 ... (remaining 17245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 18500 1.30 - 2.59: 4042 2.59 - 3.89: 521 3.89 - 5.18: 127 5.18 - 6.48: 60 Bond angle restraints: 23250 Sorted by residual: angle pdb=" C HIS m 50 " pdb=" CA HIS m 50 " pdb=" CB HIS m 50 " ideal model delta sigma weight residual 109.65 116.13 -6.48 1.75e+00 3.27e-01 1.37e+01 angle pdb=" C HIS E 50 " pdb=" CA HIS E 50 " pdb=" CB HIS E 50 " ideal model delta sigma weight residual 109.65 116.12 -6.47 1.75e+00 3.27e-01 1.37e+01 angle pdb=" C HIS 2 50 " pdb=" CA HIS 2 50 " pdb=" CB HIS 2 50 " ideal model delta sigma weight residual 109.65 116.11 -6.46 1.75e+00 3.27e-01 1.36e+01 angle pdb=" C HIS I 50 " pdb=" CA HIS I 50 " pdb=" CB HIS I 50 " ideal model delta sigma weight residual 109.65 116.11 -6.46 1.75e+00 3.27e-01 1.36e+01 angle pdb=" C HIS a 50 " pdb=" CA HIS a 50 " pdb=" CB HIS a 50 " ideal model delta sigma weight residual 109.65 116.11 -6.46 1.75e+00 3.27e-01 1.36e+01 ... (remaining 23245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11254 18.00 - 36.00: 833 36.00 - 53.99: 813 53.99 - 71.99: 342 71.99 - 89.99: 114 Dihedral angle restraints: 13356 sinusoidal: 5324 harmonic: 8032 Sorted by residual: dihedral pdb=" CA THR U 64 " pdb=" N THR U 64 " pdb=" C VAL E 63 " pdb=" CA VAL E 63 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA THR 6 64 " pdb=" N THR 6 64 " pdb=" C VAL e 63 " pdb=" CA VAL e 63 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA THR I 64 " pdb=" N THR I 64 " pdb=" C VAL q 63 " pdb=" CA VAL q 63 " ideal model delta harmonic sigma weight residual 180.00 163.27 16.73 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 13353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 964 0.028 - 0.056: 457 0.056 - 0.084: 421 0.084 - 0.112: 929 0.112 - 0.140: 289 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA ILE 7 88 " pdb=" N ILE 7 88 " pdb=" C ILE 7 88 " pdb=" CB ILE 7 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE N 88 " pdb=" N ILE N 88 " pdb=" C ILE N 88 " pdb=" CB ILE N 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE f 88 " pdb=" N ILE f 88 " pdb=" C ILE f 88 " pdb=" CB ILE f 88 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 3057 not shown) Planarity restraints: 3982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N GLN I 99 " -0.041 2.00e-02 2.50e+03 6.46e-02 4.18e+01 pdb=" CA ASP q 98 " -0.034 2.00e-02 2.50e+03 pdb=" C ASP q 98 " 0.112 2.00e-02 2.50e+03 pdb=" O ASP q 98 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N GLN 6 99 " -0.041 2.00e-02 2.50e+03 6.44e-02 4.14e+01 pdb=" CA ASP e 98 " -0.034 2.00e-02 2.50e+03 pdb=" C ASP e 98 " 0.111 2.00e-02 2.50e+03 pdb=" O ASP e 98 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N GLN U 99 " -0.041 2.00e-02 2.50e+03 6.43e-02 4.14e+01 pdb=" CA ASP E 98 " -0.034 2.00e-02 2.50e+03 pdb=" C ASP E 98 " 0.111 2.00e-02 2.50e+03 pdb=" O ASP E 98 " -0.037 2.00e-02 2.50e+03 ... (remaining 3979 not shown) Histogram of nonbonded interaction distances: 0.05 - 1.02: 10975 1.02 - 1.99: 24124 1.99 - 2.96: 51151 2.96 - 3.93: 110724 3.93 - 4.90: 242382 Warning: very small nonbonded interaction distances. Nonbonded interactions: 439356 Sorted by model distance: nonbonded pdb=" OE1 GLN V 24 " pdb=" OE1 GLN Z 24 " model vdw 0.052 3.040 nonbonded pdb=" OE1 GLN b 24 " pdb=" OE1 GLN r 24 " model vdw 0.052 3.040 nonbonded pdb=" OE1 GLN j 24 " pdb=" OE1 GLN n 24 " model vdw 0.053 3.040 nonbonded pdb=" OE1 GLN Z 24 " pdb=" OE1 GLN F 24 " model vdw 0.053 3.040 nonbonded pdb=" OE1 GLN N 24 " pdb=" OE1 GLN 3 24 " model vdw 0.053 3.040 ... (remaining 439351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '4' selection = chain '5' selection = chain '8' selection = chain '9' selection = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'c' selection = chain 'd' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'p' selection = chain 's' selection = chain 't' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain '2' selection = chain '3' selection = chain '6' selection = chain '7' selection = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'n' selection = chain 'q' selection = chain 'r' selection = chain 'u' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.570 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 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 : 0.029 0.404 18322 Z= 2.073 Angle : 2.624 22.715 26466 Z= 1.497 Chirality : 0.074 0.140 3060 Planarity : 0.003 0.011 2910 Dihedral : 8.963 47.901 5700 Min Nonbonded Distance : 0.052 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.14), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.11), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR v 39 PHE 0.010 0.003 PHE v 94 HIS 0.005 0.002 HIS U 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00815 / 0.55 (17250) covalent geometry : angle 1.13803 / 0.69 (23250) link_TRANS : bond 0.11603 / 7.94 ( 1072) link_TRANS : angle 6.87801 / 4.57 ( 3216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 58 LYS cc_start: 0.8296 (mttt) cc_final: 0.8067 (mttp) REVERT: Q 97 LYS cc_start: 0.7843 (mttt) cc_final: 0.7605 (mttm) REVERT: R 21 LYS cc_start: 0.8251 (tttt) cc_final: 0.7780 (ttpm) REVERT: R 97 LYS cc_start: 0.7937 (mttt) cc_final: 0.7670 (mttm) REVERT: u 21 LYS cc_start: 0.8089 (tttt) cc_final: 0.7500 (ttpt) REVERT: u 80 LYS cc_start: 0.8505 (tttt) cc_final: 0.6872 (mptt) REVERT: v 80 LYS cc_start: 0.8462 (tttt) cc_final: 0.6818 (mptt) REVERT: v 97 LYS cc_start: 0.7835 (mttt) cc_final: 0.7522 (mttm) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.6268 time to fit residues: 360.0196 Evaluate side-chains 509 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 40.0000 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 50.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 40.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN ** N 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 GLN ** Q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 24 GLN ** Y 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 24 GLN ** 3 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 24 GLN ** i 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 24 GLN ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 24 GLN ** n 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 79 GLN ** q 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 24 GLN ** v 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 62 GLN ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7352 r_free = 0.7352 target = 0.749441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.7473 r_free = 0.7473 target = 0.727431 restraints weight = 40116.599| |-----------------------------------------------------------------------------| r_work (start): 0.7330 rms_B_bonded: 1.26 r_work: 0.7554 rms_B_bonded: 0.46 restraints_weight: 0.5000 r_work: 0.7521 rms_B_bonded: 1.00 restraints_weight: 0.2500 r_work (final): 0.7521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1480 moved from start: 4.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.132 2.387 18322 Z= 7.974 Angle : 11.095 107.514 26466 Z= 6.522 Chirality : 0.460 3.711 3060 Planarity : 0.082 0.237 2910 Dihedral : 43.585 153.081 2520 Min Nonbonded Distance : 1.153 Molprobity Statistics. All-atom Clashscore : 818.73 Ramachandran Plot: Outliers : 41.09 % Allowed : 25.87 % Favored : 33.04 % Rotamer: Outliers : 36.73 % Allowed : 15.79 % Favored : 47.48 % Cbeta Deviations : 41.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 52.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.26 (0.09), residues: 2188 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.29 (0.07), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.182 0.027 TYR r 39 PHE 0.171 0.031 PHE E 94 HIS 0.048 0.012 HIS e 50 Details of bonding type rmsd/Z covalent geometry : bond 0.12475 / 7.24 (17250) covalent geometry : angle 10.52567 / 6.26 (23250) link_TRANS : bond 0.21891 / 14.83 ( 1072) link_TRANS : angle 14.56490 / 9.76 ( 3216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4376 Ramachandran restraints generated. 2188 Oldfield, 0 Emsley, 2188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 584 poor density : 141 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 40 VAL cc_start: 0.1187 (OUTLIER) cc_final: 0.0913 (t) REVERT: N 50 HIS cc_start: 0.2651 (OUTLIER) cc_final: 0.2365 (t-170) REVERT: U 87 SER cc_start: -0.0238 (OUTLIER) cc_final: -0.1171 (m) REVERT: V 75 THR cc_start: 0.2130 (OUTLIER) cc_final: 0.1791 (m) REVERT: V 87 SER cc_start: -0.0780 (OUTLIER) cc_final: -0.1688 (m) REVERT: Y 40 VAL cc_start: -0.2198 (OUTLIER) cc_final: -0.2407 (t) REVERT: Z 40 VAL cc_start: -0.2446 (OUTLIER) cc_final: -0.2665 (t) REVERT: E 22 THR cc_start: 0.1033 (OUTLIER) cc_final: 0.0754 (m) REVERT: a 40 VAL cc_start: -0.0680 (OUTLIER) cc_final: -0.0890 (t) REVERT: i 21 LYS cc_start: 0.4077 (OUTLIER) cc_final: 0.3448 (tttt) REVERT: j 21 LYS cc_start: 0.4625 (OUTLIER) cc_final: 0.4076 (tttt) REVERT: q 98 ASP cc_start: 0.1528 (OUTLIER) cc_final: 0.0249 (t70) REVERT: r 99 GLN cc_start: -0.1380 (OUTLIER) cc_final: -0.1687 (pm20) outliers start: 584 outliers final: 297 residues processed: 677 average time/residue: 0.3515 time to fit residues: 287.3451 Evaluate side-chains 405 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 310 poor density : 95 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 50 HIS Chi-restraints excluded: chain M residue 65 ASN Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 40 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 50 HIS Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 94 PHE Chi-restraints excluded: chain Q residue 98 ASP Chi-restraints excluded: chain R residue 94 PHE Chi-restraints excluded: chain R residue 98 ASP Chi-restraints excluded: chain U residue 15 VAL Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 39 TYR Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 57 GLU Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 75 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 20 GLU Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 59 THR Chi-restraints excluded: chain Y residue 60 LYS Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain Y residue 92 THR Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 20 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 62 GLN Chi-restraints excluded: chain Z residue 64 THR Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 100 LEU Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 20 GLU Chi-restraints excluded: chain 2 residue 23 LYS Chi-restraints excluded: chain 2 residue 65 ASN Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 98 ASP Chi-restraints excluded: chain 3 residue 23 LYS Chi-restraints excluded: chain 3 residue 38 LEU Chi-restraints excluded: chain 3 residue 46 GLU Chi-restraints excluded: chain 3 residue 62 GLN Chi-restraints excluded: chain 3 residue 64 THR Chi-restraints excluded: chain 3 residue 65 ASN Chi-restraints excluded: chain 3 residue 77 VAL Chi-restraints excluded: chain 3 residue 98 ASP Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 16 VAL Chi-restraints excluded: chain 6 residue 24 GLN Chi-restraints excluded: chain 6 residue 39 TYR Chi-restraints excluded: chain 6 residue 43 LYS Chi-restraints excluded: chain 6 residue 44 THR Chi-restraints excluded: chain 6 residue 64 THR Chi-restraints excluded: chain 6 residue 74 VAL Chi-restraints excluded: chain 6 residue 75 THR Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 79 GLN Chi-restraints excluded: chain 6 residue 80 LYS Chi-restraints excluded: chain 6 residue 81 THR Chi-restraints excluded: chain 6 residue 92 THR Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 16 VAL Chi-restraints excluded: chain 7 residue 39 TYR Chi-restraints excluded: chain 7 residue 52 VAL Chi-restraints excluded: chain 7 residue 54 THR Chi-restraints excluded: chain 7 residue 57 GLU Chi-restraints excluded: chain 7 residue 65 ASN Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 75 THR Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 79 GLN Chi-restraints excluded: chain 7 residue 80 LYS Chi-restraints excluded: chain 7 residue 81 THR Chi-restraints excluded: chain 7 residue 83 GLU Chi-restraints excluded: chain 7 residue 92 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 94 PHE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 24 GLN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 50 HIS Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 65 ASN Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 39 TYR Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 55 VAL Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 75 THR Chi-restraints excluded: chain a residue 79 GLN Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain a residue 94 PHE Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 55 VAL Chi-restraints excluded: chain b residue 62 GLN Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 92 THR Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 16 VAL Chi-restraints excluded: chain e residue 24 GLN Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 43 LYS Chi-restraints excluded: chain e residue 46 GLU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 54 THR Chi-restraints excluded: chain e residue 57 GLU Chi-restraints excluded: chain e residue 63 VAL Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 24 GLN Chi-restraints excluded: chain f residue 37 VAL Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 50 HIS Chi-restraints excluded: chain f residue 54 THR Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 81 THR Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain f residue 95 VAL Chi-restraints excluded: chain i residue 21 LYS Chi-restraints excluded: chain i residue 24 GLN Chi-restraints excluded: chain i residue 39 TYR Chi-restraints excluded: chain i residue 43 LYS Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 92 THR Chi-restraints excluded: chain i residue 96 LYS Chi-restraints excluded: chain i residue 97 LYS Chi-restraints excluded: chain i residue 100 LEU Chi-restraints excluded: chain j residue 21 LYS Chi-restraints excluded: chain j residue 38 LEU Chi-restraints excluded: chain j residue 39 TYR Chi-restraints excluded: chain j residue 43 LYS Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 50 HIS Chi-restraints excluded: chain j residue 61 GLU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 79 GLN Chi-restraints excluded: chain j residue 96 LYS Chi-restraints excluded: chain j residue 100 LEU Chi-restraints excluded: chain m residue 20 GLU Chi-restraints excluded: chain m residue 22 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 75 THR Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 20 GLU Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 63 VAL Chi-restraints excluded: chain n residue 72 THR Chi-restraints excluded: chain n residue 82 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 23 LYS Chi-restraints excluded: chain q residue 37 VAL Chi-restraints excluded: chain q residue 48 VAL Chi-restraints excluded: chain q residue 59 THR Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 74 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain q residue 98 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 24 GLN Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 45 LYS Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 52 VAL Chi-restraints excluded: chain r residue 54 THR Chi-restraints excluded: chain r residue 57 GLU Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 70 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 77 VAL Chi-restraints excluded: chain r residue 82 VAL Chi-restraints excluded: chain r residue 87 SER Chi-restraints excluded: chain r residue 88 ILE Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 98 ASP Chi-restraints excluded: chain r residue 99 GLN Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain u residue 38 LEU Chi-restraints excluded: chain u residue 64 THR Chi-restraints excluded: chain v residue 38 LEU Chi-restraints excluded: chain v residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 6 optimal weight: 30.0000 chunk 125 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 91 optimal weight: 50.0000 chunk 25 optimal weight: 0.7980 chunk 174 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 30.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN ** R 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN ** Z 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 24 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 24 GLN ** 3 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 GLN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 24 GLN ** i 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 24 GLN ** m 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 24 GLN ** u 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7320 r_free = 0.7320 target = 0.745979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.7520 r_free = 0.7520 target = 0.723721 restraints weight = 31633.740| |-----------------------------------------------------------------------------| r_work (start): 0.7314 rms_B_bonded: 0.80 r_work: 0.7566 rms_B_bonded: 0.21 restraints_weight: 0.5000 r_work: 0.7548 rms_B_bonded: 0.44 restraints_weight: 0.2500 r_work: 0.7408 rms_B_bonded: 2.71 restraints_weight: 0.1250 r_work (final): 0.7408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0925 moved from start: 5.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.111 2.205 18322 Z= 6.976 Angle : 10.101 106.763 26466 Z= 5.971 Chirality : 0.324 3.906 3060 Planarity : 0.081 0.239 2910 Dihedral : 45.019 169.546 2520 Min Nonbonded Distance : 1.224 Molprobity Statistics. All-atom Clashscore : 630.70 Ramachandran Plot: Outliers : 36.89 % Allowed : 31.28 % Favored : 31.83 % Rotamer: Outliers : 32.83 % Allowed : 22.20 % Favored : 44.97 % Cbeta Deviations : 31.80 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 53.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.42 (0.09), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.41 (0.07), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.126 0.020 TYR a 39 PHE 0.120 0.020 PHE E 94 HIS 0.039 0.010 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.10135 / 6.15 (17250) covalent geometry : angle 9.49258 / 5.69 (23250) link_TRANS : bond 0.20871 / 14.21 ( 1072) link_TRANS : angle 13.71718 / 9.20 ( 3216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 522 poor density : 90 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 79 GLN cc_start: 0.3319 (OUTLIER) cc_final: 0.3103 (mt0) REVERT: U 74 VAL cc_start: -0.1186 (OUTLIER) cc_final: -0.1665 (m) REVERT: U 80 LYS cc_start: 0.1734 (OUTLIER) cc_final: 0.1326 (tptt) REVERT: U 87 SER cc_start: -0.0057 (OUTLIER) cc_final: -0.0616 (p) REVERT: V 80 LYS cc_start: -0.0026 (OUTLIER) cc_final: -0.0308 (tptt) REVERT: V 87 SER cc_start: -0.0459 (OUTLIER) cc_final: -0.1103 (m) REVERT: Z 42 SER cc_start: -0.0849 (OUTLIER) cc_final: -0.1959 (p) REVERT: Z 81 THR cc_start: -0.0619 (OUTLIER) cc_final: -0.1076 (m) REVERT: F 95 VAL cc_start: -0.0016 (OUTLIER) cc_final: -0.0237 (t) REVERT: e 45 LYS cc_start: 0.1058 (OUTLIER) cc_final: -0.0329 (pttm) REVERT: f 39 TYR cc_start: 0.1943 (OUTLIER) cc_final: 0.1247 (t80) REVERT: q 75 THR cc_start: -0.1738 (OUTLIER) cc_final: -0.2774 (t) REVERT: q 77 VAL cc_start: -0.0187 (OUTLIER) cc_final: -0.0421 (t) REVERT: q 92 THR cc_start: 0.0307 (OUTLIER) cc_final: -0.0402 (p) REVERT: v 81 THR cc_start: 0.5157 (m) cc_final: 0.4500 (t) outliers start: 522 outliers final: 252 residues processed: 581 average time/residue: 0.4007 time to fit residues: 277.8490 Evaluate side-chains 325 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 59 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 50 HIS Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 94 PHE Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 57 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 94 PHE Chi-restraints excluded: chain Q residue 57 GLU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 79 GLN Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 37 VAL Chi-restraints excluded: chain U residue 39 TYR Chi-restraints excluded: chain U residue 45 LYS Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 57 GLU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 92 THR Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 37 VAL Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 59 THR Chi-restraints excluded: chain V residue 61 GLU Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 80 LYS Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 54 THR Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 48 VAL Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 65 ASN Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 98 ASP Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 58 LYS Chi-restraints excluded: chain 2 residue 65 ASN Chi-restraints excluded: chain 2 residue 79 GLN Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 20 GLU Chi-restraints excluded: chain 3 residue 24 GLN Chi-restraints excluded: chain 3 residue 48 VAL Chi-restraints excluded: chain 3 residue 50 HIS Chi-restraints excluded: chain 3 residue 58 LYS Chi-restraints excluded: chain 3 residue 62 GLN Chi-restraints excluded: chain 3 residue 64 THR Chi-restraints excluded: chain 3 residue 65 ASN Chi-restraints excluded: chain 3 residue 79 GLN Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 16 VAL Chi-restraints excluded: chain 6 residue 21 LYS Chi-restraints excluded: chain 6 residue 22 THR Chi-restraints excluded: chain 6 residue 24 GLN Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 39 TYR Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 71 VAL Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 87 SER Chi-restraints excluded: chain 6 residue 92 THR Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 37 VAL Chi-restraints excluded: chain 7 residue 52 VAL Chi-restraints excluded: chain 7 residue 57 GLU Chi-restraints excluded: chain 7 residue 64 THR Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 81 THR Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 39 TYR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 39 TYR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 39 TYR Chi-restraints excluded: chain J residue 62 GLN Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 80 LYS Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain a residue 39 TYR Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain a residue 94 PHE Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 98 ASP Chi-restraints excluded: chain b residue 24 GLN Chi-restraints excluded: chain b residue 39 TYR Chi-restraints excluded: chain b residue 40 VAL Chi-restraints excluded: chain b residue 48 VAL Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 62 GLN Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 65 ASN Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 96 LYS Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 23 LYS Chi-restraints excluded: chain e residue 39 TYR Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 43 LYS Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 45 LYS Chi-restraints excluded: chain e residue 46 GLU Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 54 THR Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 94 PHE Chi-restraints excluded: chain e residue 95 VAL Chi-restraints excluded: chain e residue 99 GLN Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 39 TYR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 58 LYS Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 81 THR Chi-restraints excluded: chain f residue 94 PHE Chi-restraints excluded: chain f residue 95 VAL Chi-restraints excluded: chain i residue 42 SER Chi-restraints excluded: chain i residue 94 PHE Chi-restraints excluded: chain j residue 94 PHE Chi-restraints excluded: chain j residue 97 LYS Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain m residue 38 LEU Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 64 THR Chi-restraints excluded: chain m residue 66 VAL Chi-restraints excluded: chain m residue 72 THR Chi-restraints excluded: chain m residue 79 GLN Chi-restraints excluded: chain n residue 44 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 72 THR Chi-restraints excluded: chain n residue 75 THR Chi-restraints excluded: chain n residue 79 GLN Chi-restraints excluded: chain n residue 82 VAL Chi-restraints excluded: chain q residue 16 VAL Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 54 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 92 THR Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 22 THR Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 52 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 70 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 74 VAL Chi-restraints excluded: chain r residue 79 GLN Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 99 GLN Chi-restraints excluded: chain u residue 58 LYS Chi-restraints excluded: chain v residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 161 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 chunk 193 optimal weight: 50.0000 chunk 200 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 145 optimal weight: 50.0000 chunk 72 optimal weight: 50.0000 chunk 3 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 GLN ** V 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 24 GLN ** 3 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 65 ASN ** 3 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 79 GLN ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 62 GLN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 62 GLN ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7274 r_free = 0.7274 target = 0.736825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.7445 r_free = 0.7445 target = 0.715273 restraints weight = 31234.428| |-----------------------------------------------------------------------------| r_work (start): 0.7267 rms_B_bonded: 0.73 r_work: 0.7498 rms_B_bonded: 0.23 restraints_weight: 0.5000 r_work: 0.7485 rms_B_bonded: 0.43 restraints_weight: 0.2500 r_work: 0.7369 rms_B_bonded: 2.45 restraints_weight: 0.1250 r_work (final): 0.7369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1542 moved from start: 6.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.106 2.090 18322 Z= 6.698 Angle : 9.723 108.729 26466 Z= 5.755 Chirality : 0.283 3.001 3060 Planarity : 0.081 0.247 2910 Dihedral : 45.498 179.105 2520 Min Nonbonded Distance : 1.223 Molprobity Statistics. All-atom Clashscore : 541.55 Ramachandran Plot: Outliers : 35.80 % Allowed : 31.87 % Favored : 32.33 % Rotamer: Outliers : 32.33 % Allowed : 22.52 % Favored : 45.16 % Cbeta Deviations : 26.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.36 % Twisted Proline : 0.00 % Twisted General : 54.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.35 (0.09), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.36 (0.07), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.188 0.019 TYR U 39 PHE 0.113 0.014 PHE E 94 HIS 0.033 0.008 HIS f 50 Details of bonding type rmsd/Z covalent geometry : bond 0.09640 / 5.83 (17250) covalent geometry : angle 9.11015 / 5.47 (23250) link_TRANS : bond 0.20712 / 14.08 ( 1072) link_TRANS : angle 13.33889 / 8.94 ( 3216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 514 poor density : 128 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 20 GLU cc_start: 0.0285 (OUTLIER) cc_final: 0.0015 (tp30) REVERT: V 79 GLN cc_start: 0.2279 (OUTLIER) cc_final: 0.1505 (mt0) REVERT: V 87 SER cc_start: 0.0484 (OUTLIER) cc_final: 0.0077 (m) REVERT: Y 79 GLN cc_start: 0.3089 (OUTLIER) cc_final: 0.2260 (pm20) REVERT: Z 42 SER cc_start: -0.0833 (OUTLIER) cc_final: -0.1475 (m) REVERT: Z 65 ASN cc_start: 0.2713 (OUTLIER) cc_final: 0.1997 (p0) REVERT: Z 79 GLN cc_start: 0.1590 (OUTLIER) cc_final: 0.1290 (mp10) REVERT: 2 65 ASN cc_start: 0.2629 (t0) cc_final: 0.2196 (t0) REVERT: E 21 LYS cc_start: 0.3519 (OUTLIER) cc_final: 0.3038 (ttpt) REVERT: E 58 LYS cc_start: 0.2097 (OUTLIER) cc_final: 0.1416 (pttt) REVERT: a 46 GLU cc_start: 0.0300 (OUTLIER) cc_final: -0.0836 (pp20) REVERT: a 65 ASN cc_start: -0.1201 (OUTLIER) cc_final: -0.1950 (t0) REVERT: b 46 GLU cc_start: 0.1276 (OUTLIER) cc_final: -0.0527 (mm-30) REVERT: e 62 GLN cc_start: 0.3408 (OUTLIER) cc_final: 0.2676 (mt0) REVERT: j 65 ASN cc_start: 0.4363 (t0) cc_final: 0.3878 (t0) REVERT: j 70 VAL cc_start: 0.2370 (t) cc_final: 0.2115 (t) outliers start: 514 outliers final: 232 residues processed: 605 average time/residue: 0.3635 time to fit residues: 263.4546 Evaluate side-chains 326 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 81 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 TYR Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 50 HIS Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 64 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 96 LYS Chi-restraints excluded: chain N residue 39 TYR Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 98 ASP Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain U residue 20 GLU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 80 LYS Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain V residue 20 GLU Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 52 VAL Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 94 PHE Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 100 LEU Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 65 ASN Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 79 GLN Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 100 LEU Chi-restraints excluded: chain 2 residue 23 LYS Chi-restraints excluded: chain 2 residue 50 HIS Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 79 GLN Chi-restraints excluded: chain 3 residue 15 VAL Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 45 LYS Chi-restraints excluded: chain 3 residue 46 GLU Chi-restraints excluded: chain 3 residue 50 HIS Chi-restraints excluded: chain 3 residue 77 VAL Chi-restraints excluded: chain 3 residue 79 GLN Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 21 LYS Chi-restraints excluded: chain 6 residue 52 VAL Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 71 VAL Chi-restraints excluded: chain 6 residue 72 THR Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 80 LYS Chi-restraints excluded: chain 6 residue 82 VAL Chi-restraints excluded: chain 6 residue 87 SER Chi-restraints excluded: chain 6 residue 95 VAL Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 22 THR Chi-restraints excluded: chain 7 residue 39 TYR Chi-restraints excluded: chain 7 residue 52 VAL Chi-restraints excluded: chain 7 residue 54 THR Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain 7 residue 95 VAL Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain E residue 21 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 39 TYR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 39 TYR Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 37 VAL Chi-restraints excluded: chain a residue 42 SER Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 64 THR Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 79 GLN Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain b residue 39 TYR Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 52 VAL Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain e residue 15 VAL Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 39 TYR Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 43 LYS Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 54 THR Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 62 GLN Chi-restraints excluded: chain e residue 66 VAL Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 75 THR Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 94 PHE Chi-restraints excluded: chain e residue 99 GLN Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 LYS Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 55 VAL Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 81 THR Chi-restraints excluded: chain f residue 88 ILE Chi-restraints excluded: chain f residue 94 PHE Chi-restraints excluded: chain i residue 21 LYS Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 88 ILE Chi-restraints excluded: chain i residue 94 PHE Chi-restraints excluded: chain j residue 21 LYS Chi-restraints excluded: chain j residue 79 GLN Chi-restraints excluded: chain m residue 20 GLU Chi-restraints excluded: chain m residue 38 LEU Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain m residue 58 LYS Chi-restraints excluded: chain m residue 79 GLN Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 44 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain n residue 79 GLN Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 38 LEU Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 54 THR Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 88 ILE Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 52 VAL Chi-restraints excluded: chain r residue 57 GLU Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 79 GLN Chi-restraints excluded: chain r residue 98 ASP Chi-restraints excluded: chain r residue 99 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 116 optimal weight: 40.0000 chunk 107 optimal weight: 30.0000 chunk 96 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 134 optimal weight: 40.0000 chunk 91 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 174 optimal weight: 8.9990 chunk 44 optimal weight: 30.0000 chunk 198 optimal weight: 9.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 HIS ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 65 ASN ** 3 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 79 GLN 6 24 GLN ** 6 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 24 GLN b 50 HIS ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 62 GLN ** j 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 24 GLN ** q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 50 HIS u 62 GLN ** u 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7252 r_free = 0.7252 target = 0.724525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.7403 r_free = 0.7403 target = 0.701478 restraints weight = 29723.160| |-----------------------------------------------------------------------------| r_work (start): 0.7241 rms_B_bonded: 0.90 r_work: 0.7464 rms_B_bonded: 0.27 restraints_weight: 0.5000 r_work: 0.7449 rms_B_bonded: 0.51 restraints_weight: 0.2500 r_work: 0.7313 rms_B_bonded: 2.96 restraints_weight: 0.1250 r_work (final): 0.7313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2103 moved from start: 6.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.104 2.067 18322 Z= 6.556 Angle : 9.593 100.311 26466 Z= 5.680 Chirality : 0.274 1.951 3060 Planarity : 0.081 0.255 2910 Dihedral : 45.160 173.814 2520 Min Nonbonded Distance : 1.265 Molprobity Statistics. All-atom Clashscore : 518.68 Ramachandran Plot: Outliers : 35.07 % Allowed : 32.65 % Favored : 32.28 % Rotamer: Outliers : 27.42 % Allowed : 24.15 % Favored : 48.43 % Cbeta Deviations : 25.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 54.44 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.22 (0.10), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.26 (0.07), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.185 0.016 TYR U 39 PHE 0.102 0.015 PHE m 94 HIS 0.042 0.008 HIS e 50 Details of bonding type rmsd/Z covalent geometry : bond 0.09440 / 5.71 (17250) covalent geometry : angle 8.95106 / 5.38 (23250) link_TRANS : bond 0.20280 / 13.74 ( 1072) link_TRANS : angle 13.34468 / 8.95 ( 3216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 436 poor density : 109 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 61 GLU cc_start: 0.3783 (OUTLIER) cc_final: 0.2901 (mt-10) REVERT: N 80 LYS cc_start: -0.0320 (OUTLIER) cc_final: -0.1521 (mppt) REVERT: 2 65 ASN cc_start: 0.3394 (t0) cc_final: 0.3053 (t0) REVERT: 7 21 LYS cc_start: 0.0435 (OUTLIER) cc_final: -0.0690 (mptt) REVERT: 7 65 ASN cc_start: 0.1198 (OUTLIER) cc_final: 0.0853 (p0) REVERT: A 98 ASP cc_start: 0.5529 (OUTLIER) cc_final: 0.5133 (m-30) REVERT: E 58 LYS cc_start: 0.1852 (OUTLIER) cc_final: 0.1540 (ttpp) REVERT: E 61 GLU cc_start: 0.2061 (OUTLIER) cc_final: 0.1379 (mt-10) REVERT: I 77 VAL cc_start: 0.0191 (OUTLIER) cc_final: -0.0133 (m) REVERT: J 15 VAL cc_start: -0.1136 (OUTLIER) cc_final: -0.1337 (t) REVERT: a 65 ASN cc_start: -0.0957 (OUTLIER) cc_final: -0.1408 (t0) REVERT: b 15 VAL cc_start: -0.0330 (OUTLIER) cc_final: -0.1988 (p) REVERT: e 62 GLN cc_start: 0.3084 (OUTLIER) cc_final: 0.1973 (mt0) REVERT: i 65 ASN cc_start: 0.3959 (t0) cc_final: 0.3505 (t0) REVERT: j 65 ASN cc_start: 0.3997 (t0) cc_final: 0.3261 (t0) REVERT: n 58 LYS cc_start: -0.0042 (OUTLIER) cc_final: -0.0411 (pptt) REVERT: r 46 GLU cc_start: 0.1736 (OUTLIER) cc_final: 0.1410 (mt-10) outliers start: 436 outliers final: 225 residues processed: 519 average time/residue: 0.3824 time to fit residues: 236.1624 Evaluate side-chains 325 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 86 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 64 THR Chi-restraints excluded: chain N residue 80 LYS Chi-restraints excluded: chain N residue 96 LYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 20 GLU Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 62 GLN Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain V residue 87 SER Chi-restraints excluded: chain Y residue 42 SER Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 64 THR Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain Y residue 79 GLN Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 82 VAL Chi-restraints excluded: chain Y residue 94 PHE Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Z residue 39 TYR Chi-restraints excluded: chain Z residue 49 VAL Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 77 VAL Chi-restraints excluded: chain Z residue 79 GLN Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 24 GLN Chi-restraints excluded: chain 2 residue 50 HIS Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 75 THR Chi-restraints excluded: chain 2 residue 79 GLN Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 46 GLU Chi-restraints excluded: chain 3 residue 50 HIS Chi-restraints excluded: chain 3 residue 54 THR Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 21 LYS Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 48 VAL Chi-restraints excluded: chain 6 residue 52 VAL Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 80 LYS Chi-restraints excluded: chain 6 residue 81 THR Chi-restraints excluded: chain 6 residue 87 SER Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 21 LYS Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 44 THR Chi-restraints excluded: chain 7 residue 54 THR Chi-restraints excluded: chain 7 residue 64 THR Chi-restraints excluded: chain 7 residue 65 ASN Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 81 THR Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 58 LYS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 79 GLN Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 39 TYR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 79 GLN Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain a residue 95 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 39 TYR Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 79 GLN Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 98 ASP Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 44 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 62 GLN Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 94 PHE Chi-restraints excluded: chain e residue 99 GLN Chi-restraints excluded: chain f residue 15 VAL Chi-restraints excluded: chain f residue 22 THR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 45 LYS Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 62 GLN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 80 LYS Chi-restraints excluded: chain f residue 94 PHE Chi-restraints excluded: chain f residue 96 LYS Chi-restraints excluded: chain i residue 38 LEU Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 54 THR Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 79 GLN Chi-restraints excluded: chain i residue 92 THR Chi-restraints excluded: chain i residue 94 PHE Chi-restraints excluded: chain j residue 37 VAL Chi-restraints excluded: chain j residue 62 GLN Chi-restraints excluded: chain j residue 79 GLN Chi-restraints excluded: chain j residue 80 LYS Chi-restraints excluded: chain j residue 94 PHE Chi-restraints excluded: chain m residue 24 GLN Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain m residue 65 ASN Chi-restraints excluded: chain m residue 79 GLN Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 40 VAL Chi-restraints excluded: chain n residue 44 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 45 LYS Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 94 PHE Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 59 THR Chi-restraints excluded: chain r residue 70 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 98 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 97 LYS Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 97 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 99 GLN R 62 GLN ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 79 GLN ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 65 ASN ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7221 r_free = 0.7221 target = 0.716185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.7308 r_free = 0.7308 target = 0.693820 restraints weight = 29392.217| |-----------------------------------------------------------------------------| r_work (start): 0.7200 rms_B_bonded: 1.30 r_work: 0.7407 rms_B_bonded: 0.38 restraints_weight: 0.5000 r_work: 0.7382 rms_B_bonded: 0.76 restraints_weight: 0.2500 r_work: 0.7315 rms_B_bonded: 2.89 restraints_weight: 0.1250 r_work (final): 0.7315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2314 moved from start: 6.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.102 2.014 18322 Z= 6.457 Angle : 9.521 100.222 26466 Z= 5.641 Chirality : 0.277 1.851 3060 Planarity : 0.081 0.256 2910 Dihedral : 45.129 169.350 2520 Min Nonbonded Distance : 1.250 Molprobity Statistics. All-atom Clashscore : 512.94 Ramachandran Plot: Outliers : 34.16 % Allowed : 33.06 % Favored : 32.79 % Rotamer: Outliers : 24.34 % Allowed : 27.04 % Favored : 48.62 % Cbeta Deviations : 24.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 55.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.13 (0.10), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.19 (0.07), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.223 0.015 TYR U 39 PHE 0.100 0.015 PHE m 94 HIS 0.047 0.009 HIS f 50 Details of bonding type rmsd/Z covalent geometry : bond 0.09307 / 5.63 (17250) covalent geometry : angle 8.87524 / 5.34 (23250) link_TRANS : bond 0.19960 / 13.52 ( 1072) link_TRANS : angle 13.28415 / 8.92 ( 3216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 387 poor density : 106 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 42 SER cc_start: 0.0969 (OUTLIER) cc_final: 0.0356 (t) REVERT: U 66 VAL cc_start: 0.0542 (OUTLIER) cc_final: 0.0282 (m) REVERT: U 79 GLN cc_start: 0.3125 (OUTLIER) cc_final: 0.2558 (mt0) REVERT: V 21 LYS cc_start: 0.1139 (OUTLIER) cc_final: -0.0132 (mptt) REVERT: V 39 TYR cc_start: 0.1174 (OUTLIER) cc_final: 0.0562 (t80) REVERT: 2 65 ASN cc_start: 0.2874 (t0) cc_final: 0.2651 (t0) REVERT: 6 20 GLU cc_start: 0.1335 (OUTLIER) cc_final: 0.0743 (tp30) REVERT: 7 20 GLU cc_start: 0.1052 (OUTLIER) cc_final: 0.0551 (mp0) REVERT: A 39 TYR cc_start: -0.0437 (OUTLIER) cc_final: -0.0862 (t80) REVERT: A 98 ASP cc_start: 0.5586 (OUTLIER) cc_final: 0.5194 (m-30) REVERT: C 50 HIS cc_start: 0.0463 (OUTLIER) cc_final: 0.0149 (m90) REVERT: E 54 THR cc_start: 0.1599 (OUTLIER) cc_final: 0.1027 (m) REVERT: E 71 VAL cc_start: 0.4235 (OUTLIER) cc_final: 0.3998 (t) REVERT: F 50 HIS cc_start: -0.0490 (OUTLIER) cc_final: -0.0822 (t70) REVERT: I 21 LYS cc_start: 0.0092 (OUTLIER) cc_final: -0.1028 (mtpt) REVERT: I 65 ASN cc_start: 0.3356 (OUTLIER) cc_final: 0.2998 (t0) REVERT: J 15 VAL cc_start: -0.0936 (OUTLIER) cc_final: -0.1230 (t) REVERT: a 46 GLU cc_start: 0.0623 (OUTLIER) cc_final: -0.0327 (pm20) REVERT: a 65 ASN cc_start: -0.0455 (OUTLIER) cc_final: -0.1467 (t0) REVERT: a 81 THR cc_start: -0.0910 (OUTLIER) cc_final: -0.1143 (p) REVERT: b 15 VAL cc_start: -0.0213 (OUTLIER) cc_final: -0.2194 (p) REVERT: f 23 LYS cc_start: 0.4172 (tmtt) cc_final: 0.3923 (tmtt) REVERT: f 59 THR cc_start: 0.1712 (OUTLIER) cc_final: 0.1373 (m) REVERT: i 79 GLN cc_start: 0.5456 (OUTLIER) cc_final: 0.4448 (pt0) REVERT: j 65 ASN cc_start: 0.3503 (t0) cc_final: 0.3106 (t0) REVERT: m 43 LYS cc_start: 0.1214 (tptt) cc_final: 0.0572 (pmtt) REVERT: q 94 PHE cc_start: 0.1296 (OUTLIER) cc_final: 0.0715 (p90) REVERT: r 46 GLU cc_start: 0.1806 (OUTLIER) cc_final: 0.1431 (mt-10) outliers start: 387 outliers final: 215 residues processed: 467 average time/residue: 0.4005 time to fit residues: 221.7325 Evaluate side-chains 332 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 93 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 50 HIS Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 96 LYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 80 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 62 GLN Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 16 VAL Chi-restraints excluded: chain V residue 21 LYS Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 79 GLN Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 94 PHE Chi-restraints excluded: chain Z residue 71 VAL Chi-restraints excluded: chain Z residue 79 GLN Chi-restraints excluded: chain 2 residue 15 VAL Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 23 LYS Chi-restraints excluded: chain 2 residue 42 SER Chi-restraints excluded: chain 2 residue 45 LYS Chi-restraints excluded: chain 2 residue 50 HIS Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 79 GLN Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 50 HIS Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 20 GLU Chi-restraints excluded: chain 6 residue 21 LYS Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 48 VAL Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 62 GLN Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 81 THR Chi-restraints excluded: chain 6 residue 87 SER Chi-restraints excluded: chain 6 residue 100 LEU Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 20 GLU Chi-restraints excluded: chain 7 residue 21 LYS Chi-restraints excluded: chain 7 residue 22 THR Chi-restraints excluded: chain 7 residue 37 VAL Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 44 THR Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 52 VAL Chi-restraints excluded: chain 7 residue 54 THR Chi-restraints excluded: chain 7 residue 64 THR Chi-restraints excluded: chain 7 residue 65 ASN Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 81 THR Chi-restraints excluded: chain 7 residue 82 VAL Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 39 TYR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 39 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 39 TYR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 64 THR Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 79 GLN Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain a residue 95 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 59 THR Chi-restraints excluded: chain b residue 62 GLN Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 77 VAL Chi-restraints excluded: chain b residue 79 GLN Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 23 LYS Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 43 LYS Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 62 GLN Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 88 ILE Chi-restraints excluded: chain e residue 94 PHE Chi-restraints excluded: chain e residue 99 GLN Chi-restraints excluded: chain f residue 45 LYS Chi-restraints excluded: chain f residue 46 GLU Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 88 ILE Chi-restraints excluded: chain f residue 94 PHE Chi-restraints excluded: chain f residue 95 VAL Chi-restraints excluded: chain i residue 24 GLN Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 79 GLN Chi-restraints excluded: chain i residue 94 PHE Chi-restraints excluded: chain i residue 96 LYS Chi-restraints excluded: chain j residue 15 VAL Chi-restraints excluded: chain j residue 21 LYS Chi-restraints excluded: chain j residue 37 VAL Chi-restraints excluded: chain j residue 45 LYS Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 79 GLN Chi-restraints excluded: chain j residue 94 PHE Chi-restraints excluded: chain m residue 40 VAL Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain m residue 65 ASN Chi-restraints excluded: chain m residue 79 GLN Chi-restraints excluded: chain m residue 82 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 23 LYS Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 40 VAL Chi-restraints excluded: chain n residue 44 THR Chi-restraints excluded: chain n residue 52 VAL Chi-restraints excluded: chain n residue 75 THR Chi-restraints excluded: chain q residue 20 GLU Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 71 VAL Chi-restraints excluded: chain q residue 72 THR Chi-restraints excluded: chain q residue 94 PHE Chi-restraints excluded: chain r residue 22 THR Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 43 LYS Chi-restraints excluded: chain r residue 46 GLU Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 52 VAL Chi-restraints excluded: chain r residue 61 GLU Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 88 ILE Chi-restraints excluded: chain r residue 98 ASP Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 64 THR Chi-restraints excluded: chain u residue 97 LYS Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 88 ILE Chi-restraints excluded: chain v residue 97 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 23 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 147 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 189 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 24 GLN ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 99 GLN ** N 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN ** Z 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 79 GLN ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 99 GLN ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7218 r_free = 0.7218 target = 0.715218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.7309 r_free = 0.7309 target = 0.693420 restraints weight = 29232.726| |-----------------------------------------------------------------------------| r_work (start): 0.7200 rms_B_bonded: 1.53 r_work: 0.7398 rms_B_bonded: 0.44 restraints_weight: 0.5000 r_work: 0.7373 rms_B_bonded: 0.93 restraints_weight: 0.2500 r_work: 0.7310 rms_B_bonded: 3.06 restraints_weight: 0.1250 r_work (final): 0.7310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2373 moved from start: 6.7541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.102 1.972 18322 Z= 6.394 Angle : 9.442 100.302 26466 Z= 5.582 Chirality : 0.281 2.288 3060 Planarity : 0.081 0.251 2910 Dihedral : 44.902 163.971 2520 Min Nonbonded Distance : 1.287 Molprobity Statistics. All-atom Clashscore : 502.61 Ramachandran Plot: Outliers : 34.25 % Allowed : 32.79 % Favored : 32.97 % Rotamer: Outliers : 21.51 % Allowed : 30.25 % Favored : 48.24 % Cbeta Deviations : 23.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 55.87 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.12 (0.10), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.18 (0.07), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.195 0.014 TYR U 39 PHE 0.085 0.013 PHE m 94 HIS 0.033 0.008 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.09248 / 5.58 (17250) covalent geometry : angle 8.79546 / 5.28 (23250) link_TRANS : bond 0.19703 / 13.32 ( 1072) link_TRANS : angle 13.20480 / 8.89 ( 3216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 342 poor density : 115 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 79 GLN cc_start: 0.3176 (OUTLIER) cc_final: 0.2713 (mt0) REVERT: V 39 TYR cc_start: 0.0781 (OUTLIER) cc_final: 0.0288 (t80) REVERT: 2 79 GLN cc_start: 0.3217 (OUTLIER) cc_final: 0.2826 (tt0) REVERT: 6 21 LYS cc_start: 0.0613 (OUTLIER) cc_final: 0.0305 (ptmt) REVERT: 7 20 GLU cc_start: 0.1420 (OUTLIER) cc_final: 0.0887 (mp0) REVERT: 7 46 GLU cc_start: 0.2789 (OUTLIER) cc_final: 0.1110 (tm-30) REVERT: A 15 VAL cc_start: -0.1303 (OUTLIER) cc_final: -0.2489 (t) REVERT: A 46 GLU cc_start: 0.1908 (OUTLIER) cc_final: 0.0726 (mp0) REVERT: A 98 ASP cc_start: 0.5869 (OUTLIER) cc_final: 0.5505 (m-30) REVERT: E 54 THR cc_start: 0.1563 (OUTLIER) cc_final: 0.0968 (t) REVERT: I 65 ASN cc_start: 0.3173 (OUTLIER) cc_final: 0.2856 (t0) REVERT: J 95 VAL cc_start: 0.0620 (OUTLIER) cc_final: 0.0154 (m) REVERT: a 15 VAL cc_start: -0.0217 (OUTLIER) cc_final: -0.1861 (m) REVERT: a 46 GLU cc_start: 0.1023 (OUTLIER) cc_final: -0.0255 (pt0) REVERT: a 65 ASN cc_start: -0.0389 (OUTLIER) cc_final: -0.1317 (t0) REVERT: b 15 VAL cc_start: -0.0166 (OUTLIER) cc_final: -0.1622 (t) REVERT: b 79 GLN cc_start: 0.2299 (OUTLIER) cc_final: 0.1857 (tp40) REVERT: e 62 GLN cc_start: 0.2059 (OUTLIER) cc_final: 0.1412 (mt0) REVERT: f 23 LYS cc_start: 0.4354 (OUTLIER) cc_final: 0.4107 (tmtt) REVERT: i 79 GLN cc_start: 0.5410 (OUTLIER) cc_final: 0.4618 (pt0) REVERT: j 65 ASN cc_start: 0.3537 (t0) cc_final: 0.2884 (t0) REVERT: m 79 GLN cc_start: 0.1277 (OUTLIER) cc_final: 0.1069 (pm20) REVERT: q 94 PHE cc_start: 0.1680 (OUTLIER) cc_final: 0.1175 (p90) REVERT: r 65 ASN cc_start: 0.0342 (OUTLIER) cc_final: -0.0293 (t0) REVERT: r 96 LYS cc_start: 0.0266 (OUTLIER) cc_final: -0.0977 (tptp) outliers start: 342 outliers final: 194 residues processed: 434 average time/residue: 0.4118 time to fit residues: 212.4119 Evaluate side-chains 320 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 102 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 50 HIS Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 99 GLN Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 80 LYS Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 87 SER Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 21 LYS Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Z residue 38 LEU Chi-restraints excluded: chain Z residue 79 GLN Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 96 LYS Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 42 SER Chi-restraints excluded: chain 2 residue 45 LYS Chi-restraints excluded: chain 2 residue 50 HIS Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 79 GLN Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 50 HIS Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 21 LYS Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 50 HIS Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 87 SER Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 20 GLU Chi-restraints excluded: chain 7 residue 21 LYS Chi-restraints excluded: chain 7 residue 37 VAL Chi-restraints excluded: chain 7 residue 42 SER Chi-restraints excluded: chain 7 residue 44 THR Chi-restraints excluded: chain 7 residue 46 GLU Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 52 VAL Chi-restraints excluded: chain 7 residue 54 THR Chi-restraints excluded: chain 7 residue 64 THR Chi-restraints excluded: chain 7 residue 65 ASN Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 81 THR Chi-restraints excluded: chain 7 residue 82 VAL Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 39 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 64 THR Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 39 TYR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 79 GLN Chi-restraints excluded: chain a residue 81 THR Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain a residue 95 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 79 GLN Chi-restraints excluded: chain b residue 81 THR Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain e residue 43 LYS Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 62 GLN Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 80 LYS Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 94 PHE Chi-restraints excluded: chain e residue 99 GLN Chi-restraints excluded: chain f residue 23 LYS Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 46 GLU Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 75 THR Chi-restraints excluded: chain f residue 88 ILE Chi-restraints excluded: chain f residue 94 PHE Chi-restraints excluded: chain f residue 95 VAL Chi-restraints excluded: chain i residue 24 GLN Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 79 GLN Chi-restraints excluded: chain j residue 37 VAL Chi-restraints excluded: chain j residue 62 GLN Chi-restraints excluded: chain j residue 79 GLN Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 40 VAL Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 79 GLN Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 44 THR Chi-restraints excluded: chain n residue 59 THR Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain n residue 77 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 39 TYR Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 49 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain q residue 70 VAL Chi-restraints excluded: chain q residue 94 PHE Chi-restraints excluded: chain r residue 22 THR Chi-restraints excluded: chain r residue 39 TYR Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 44 THR Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 52 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 65 ASN Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 88 ILE Chi-restraints excluded: chain r residue 96 LYS Chi-restraints excluded: chain r residue 98 ASP Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 64 THR Chi-restraints excluded: chain u residue 95 VAL Chi-restraints excluded: chain u residue 97 LYS Chi-restraints excluded: chain v residue 57 GLU Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 71 VAL Chi-restraints excluded: chain v residue 88 ILE Chi-restraints excluded: chain v residue 97 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 156 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 195 optimal weight: 40.0000 chunk 5 optimal weight: 6.9990 chunk 105 optimal weight: 50.0000 chunk 23 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 99 GLN Q 50 HIS ** R 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 99 GLN 3 99 GLN ** 7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7214 r_free = 0.7214 target = 0.715889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.7272 r_free = 0.7272 target = 0.694131 restraints weight = 28774.755| |-----------------------------------------------------------------------------| r_work (start): 0.7189 rms_B_bonded: 1.16 r_work: 0.7396 rms_B_bonded: 0.35 restraints_weight: 0.5000 r_work: 0.7381 rms_B_bonded: 0.66 restraints_weight: 0.2500 r_work: 0.7327 rms_B_bonded: 2.40 restraints_weight: 0.1250 r_work (final): 0.7327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2401 moved from start: 6.8567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.101 1.930 18322 Z= 6.356 Angle : 9.392 100.508 26466 Z= 5.549 Chirality : 0.274 2.024 3060 Planarity : 0.081 0.249 2910 Dihedral : 44.748 166.590 2520 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 499.23 Ramachandran Plot: Outliers : 34.25 % Allowed : 33.65 % Favored : 32.10 % Rotamer: Outliers : 19.50 % Allowed : 32.26 % Favored : 48.24 % Cbeta Deviations : 23.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 55.73 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.15 (0.10), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.21 (0.07), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.158 0.014 TYR U 39 PHE 0.098 0.013 PHE a 94 HIS 0.035 0.007 HIS e 50 Details of bonding type rmsd/Z covalent geometry : bond 0.09190 / 5.54 (17250) covalent geometry : angle 8.75922 / 5.25 (23250) link_TRANS : bond 0.19615 / 13.23 ( 1072) link_TRANS : angle 13.08892 / 8.83 ( 3216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 310 poor density : 109 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 LYS cc_start: 0.3098 (OUTLIER) cc_final: 0.2755 (mttp) REVERT: N 80 LYS cc_start: 0.1295 (OUTLIER) cc_final: 0.0753 (mptt) REVERT: Q 44 THR cc_start: 0.5966 (p) cc_final: 0.5655 (p) REVERT: U 79 GLN cc_start: 0.3337 (OUTLIER) cc_final: 0.2973 (mt0) REVERT: V 39 TYR cc_start: 0.0548 (OUTLIER) cc_final: 0.0107 (t80) REVERT: Y 39 TYR cc_start: 0.1515 (OUTLIER) cc_final: 0.1115 (m-10) REVERT: Y 60 LYS cc_start: 0.2086 (OUTLIER) cc_final: 0.1884 (mtpp) REVERT: Z 79 GLN cc_start: 0.1016 (OUTLIER) cc_final: 0.0809 (pm20) REVERT: 7 46 GLU cc_start: 0.2611 (OUTLIER) cc_final: 0.0936 (tm-30) REVERT: 7 82 VAL cc_start: -0.0167 (OUTLIER) cc_final: -0.0743 (m) REVERT: A 15 VAL cc_start: -0.0944 (OUTLIER) cc_final: -0.2338 (t) REVERT: A 46 GLU cc_start: 0.1571 (OUTLIER) cc_final: 0.1359 (mm-30) REVERT: I 96 LYS cc_start: 0.0914 (OUTLIER) cc_final: 0.0394 (pptt) REVERT: J 81 THR cc_start: -0.1365 (OUTLIER) cc_final: -0.1678 (m) REVERT: J 95 VAL cc_start: -0.0221 (OUTLIER) cc_final: -0.0533 (t) REVERT: a 15 VAL cc_start: -0.0142 (OUTLIER) cc_final: -0.1677 (m) REVERT: a 46 GLU cc_start: 0.1131 (OUTLIER) cc_final: 0.0401 (pt0) REVERT: a 65 ASN cc_start: -0.0443 (OUTLIER) cc_final: -0.0917 (t0) REVERT: a 79 GLN cc_start: 0.3070 (OUTLIER) cc_final: 0.2498 (tm130) REVERT: a 88 ILE cc_start: 0.3038 (OUTLIER) cc_final: 0.2542 (tt) REVERT: b 15 VAL cc_start: -0.0036 (OUTLIER) cc_final: -0.1357 (t) REVERT: e 65 ASN cc_start: 0.0941 (OUTLIER) cc_final: 0.0550 (t0) REVERT: f 23 LYS cc_start: 0.4518 (OUTLIER) cc_final: 0.4058 (tmtt) REVERT: i 79 GLN cc_start: 0.5402 (OUTLIER) cc_final: 0.4688 (pt0) REVERT: j 65 ASN cc_start: 0.3152 (t0) cc_final: 0.2456 (t0) REVERT: j 80 LYS cc_start: 0.2962 (OUTLIER) cc_final: 0.2710 (mmtt) REVERT: n 43 LYS cc_start: -0.0018 (OUTLIER) cc_final: -0.0348 (mmmt) REVERT: q 23 LYS cc_start: 0.4488 (OUTLIER) cc_final: 0.4032 (ttmt) REVERT: v 94 PHE cc_start: 0.2167 (OUTLIER) cc_final: 0.1553 (t80) outliers start: 310 outliers final: 188 residues processed: 393 average time/residue: 0.4095 time to fit residues: 190.9592 Evaluate side-chains 314 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 99 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 80 LYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 80 LYS Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 21 LYS Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 48 VAL Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Y residue 39 TYR Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 60 LYS Chi-restraints excluded: chain Y residue 65 ASN Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 79 GLN Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 42 SER Chi-restraints excluded: chain 2 residue 45 LYS Chi-restraints excluded: chain 2 residue 50 HIS Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 59 THR Chi-restraints excluded: chain 2 residue 79 GLN Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 21 LYS Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 50 HIS Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 58 LYS Chi-restraints excluded: chain 6 residue 64 THR Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 87 SER Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 44 THR Chi-restraints excluded: chain 7 residue 46 GLU Chi-restraints excluded: chain 7 residue 48 VAL Chi-restraints excluded: chain 7 residue 52 VAL Chi-restraints excluded: chain 7 residue 64 THR Chi-restraints excluded: chain 7 residue 65 ASN Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 81 THR Chi-restraints excluded: chain 7 residue 82 VAL Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 39 TYR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 75 THR Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 79 GLN Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain a residue 95 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 82 VAL Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 95 VAL Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 23 LYS Chi-restraints excluded: chain e residue 24 GLN Chi-restraints excluded: chain e residue 40 VAL Chi-restraints excluded: chain e residue 43 LYS Chi-restraints excluded: chain e residue 62 GLN Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 94 PHE Chi-restraints excluded: chain e residue 99 GLN Chi-restraints excluded: chain f residue 23 LYS Chi-restraints excluded: chain f residue 39 TYR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 46 GLU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 75 THR Chi-restraints excluded: chain f residue 88 ILE Chi-restraints excluded: chain f residue 94 PHE Chi-restraints excluded: chain i residue 24 GLN Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 79 GLN Chi-restraints excluded: chain j residue 37 VAL Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 79 GLN Chi-restraints excluded: chain j residue 80 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 40 VAL Chi-restraints excluded: chain m residue 44 THR Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 23 LYS Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 43 LYS Chi-restraints excluded: chain n residue 59 THR Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain n residue 77 VAL Chi-restraints excluded: chain n residue 95 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 23 LYS Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 50 HIS Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 43 LYS Chi-restraints excluded: chain r residue 44 THR Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 52 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 61 GLU Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 95 VAL Chi-restraints excluded: chain r residue 96 LYS Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 48 VAL Chi-restraints excluded: chain u residue 58 LYS Chi-restraints excluded: chain u residue 64 THR Chi-restraints excluded: chain u residue 97 LYS Chi-restraints excluded: chain v residue 57 GLU Chi-restraints excluded: chain v residue 59 THR Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 88 ILE Chi-restraints excluded: chain v residue 94 PHE Chi-restraints excluded: chain v residue 97 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 209 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 115 optimal weight: 40.0000 chunk 151 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 24 GLN ** Z 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 65 ASN 3 99 GLN 6 24 GLN ** 7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7211 r_free = 0.7211 target = 0.714993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.7278 r_free = 0.7278 target = 0.693942 restraints weight = 33818.478| |-----------------------------------------------------------------------------| r_work (start): 0.7188 rms_B_bonded: 1.80 r_work: 0.7369 rms_B_bonded: 0.56 restraints_weight: 0.5000 r_work: 0.7336 rms_B_bonded: 1.19 restraints_weight: 0.2500 r_work: 0.7261 rms_B_bonded: 4.04 restraints_weight: 0.1250 r_work (final): 0.7261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2537 moved from start: 6.9150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.101 1.935 18322 Z= 6.337 Angle : 9.341 100.563 26466 Z= 5.520 Chirality : 0.271 2.110 3060 Planarity : 0.081 0.249 2910 Dihedral : 44.615 167.029 2520 Min Nonbonded Distance : 1.238 Molprobity Statistics. All-atom Clashscore : 501.43 Ramachandran Plot: Outliers : 33.74 % Allowed : 34.89 % Favored : 31.37 % Rotamer: Outliers : 16.98 % Allowed : 34.03 % Favored : 48.99 % Cbeta Deviations : 23.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 55.78 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.19 (0.10), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.24 (0.07), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.125 0.013 TYR U 39 PHE 0.077 0.012 PHE u 94 HIS 0.038 0.007 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.09140 / 5.53 (17250) covalent geometry : angle 8.71047 / 5.22 (23250) link_TRANS : bond 0.19550 / 13.18 ( 1072) link_TRANS : angle 13.01961 / 8.76 ( 3216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 270 poor density : 100 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 LYS cc_start: 0.3674 (OUTLIER) cc_final: 0.3110 (mttp) REVERT: N 80 LYS cc_start: 0.1630 (OUTLIER) cc_final: 0.1127 (mptt) REVERT: Q 44 THR cc_start: 0.6142 (p) cc_final: 0.5931 (p) REVERT: U 79 GLN cc_start: 0.3165 (OUTLIER) cc_final: 0.2900 (mt0) REVERT: V 21 LYS cc_start: 0.1318 (OUTLIER) cc_final: 0.1104 (mptt) REVERT: V 39 TYR cc_start: 0.0503 (OUTLIER) cc_final: 0.0155 (t80) REVERT: 2 79 GLN cc_start: 0.3756 (OUTLIER) cc_final: 0.3259 (tp40) REVERT: 3 80 LYS cc_start: 0.2231 (OUTLIER) cc_final: 0.1946 (ttpt) REVERT: 7 46 GLU cc_start: 0.2228 (OUTLIER) cc_final: 0.0591 (OUTLIER) REVERT: 7 65 ASN cc_start: 0.1234 (OUTLIER) cc_final: 0.0696 (p0) REVERT: A 15 VAL cc_start: -0.0839 (OUTLIER) cc_final: -0.1751 (m) REVERT: A 46 GLU cc_start: 0.1452 (OUTLIER) cc_final: 0.1145 (mm-30) REVERT: I 65 ASN cc_start: 0.2998 (OUTLIER) cc_final: 0.2333 (t0) REVERT: I 96 LYS cc_start: 0.0668 (OUTLIER) cc_final: -0.0020 (pptt) REVERT: J 37 VAL cc_start: 0.2995 (OUTLIER) cc_final: 0.2681 (m) REVERT: a 15 VAL cc_start: 0.0159 (OUTLIER) cc_final: -0.1380 (m) REVERT: a 46 GLU cc_start: 0.0986 (OUTLIER) cc_final: 0.0638 (pt0) REVERT: a 65 ASN cc_start: -0.0646 (OUTLIER) cc_final: -0.1138 (t0) REVERT: b 15 VAL cc_start: 0.0318 (OUTLIER) cc_final: -0.1131 (t) REVERT: e 65 ASN cc_start: 0.0781 (OUTLIER) cc_final: 0.0123 (t0) REVERT: i 79 GLN cc_start: 0.5464 (OUTLIER) cc_final: 0.4946 (pt0) REVERT: q 23 LYS cc_start: 0.4445 (OUTLIER) cc_final: 0.4104 (ttmt) REVERT: r 96 LYS cc_start: 0.0556 (OUTLIER) cc_final: -0.0286 (tptp) outliers start: 270 outliers final: 165 residues processed: 347 average time/residue: 0.3493 time to fit residues: 145.3622 Evaluate side-chains 282 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 96 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 44 THR Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 80 LYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 80 LYS Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 21 LYS Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Y residue 21 LYS Chi-restraints excluded: chain Y residue 39 TYR Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 49 VAL Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 65 ASN Chi-restraints excluded: chain Z residue 82 VAL Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain 2 residue 16 VAL Chi-restraints excluded: chain 2 residue 42 SER Chi-restraints excluded: chain 2 residue 44 THR Chi-restraints excluded: chain 2 residue 50 HIS Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 79 GLN Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 21 LYS Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 50 HIS Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 58 LYS Chi-restraints excluded: chain 6 residue 64 THR Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 87 SER Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 46 GLU Chi-restraints excluded: chain 7 residue 49 VAL Chi-restraints excluded: chain 7 residue 52 VAL Chi-restraints excluded: chain 7 residue 64 THR Chi-restraints excluded: chain 7 residue 65 ASN Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 81 THR Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain E residue 39 TYR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 65 ASN Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 39 TYR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 75 THR Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 79 GLN Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain a residue 95 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain e residue 22 THR Chi-restraints excluded: chain e residue 24 GLN Chi-restraints excluded: chain e residue 43 LYS Chi-restraints excluded: chain e residue 62 GLN Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 94 PHE Chi-restraints excluded: chain e residue 99 GLN Chi-restraints excluded: chain f residue 39 TYR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 43 LYS Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 75 THR Chi-restraints excluded: chain f residue 88 ILE Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 79 GLN Chi-restraints excluded: chain j residue 37 VAL Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 79 GLN Chi-restraints excluded: chain m residue 40 VAL Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 59 THR Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain n residue 77 VAL Chi-restraints excluded: chain n residue 95 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 23 LYS Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 52 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 96 LYS Chi-restraints excluded: chain u residue 21 LYS Chi-restraints excluded: chain u residue 37 VAL Chi-restraints excluded: chain u residue 64 THR Chi-restraints excluded: chain u residue 97 LYS Chi-restraints excluded: chain v residue 57 GLU Chi-restraints excluded: chain v residue 59 THR Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 88 ILE Chi-restraints excluded: chain v residue 97 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 85 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 202 optimal weight: 0.0470 chunk 74 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 80 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 overall best weight: 5.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 GLN ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 65 ASN 6 24 GLN ** 7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7214 r_free = 0.7214 target = 0.717337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.7311 r_free = 0.7311 target = 0.695913 restraints weight = 34132.309| |-----------------------------------------------------------------------------| r_work (start): 0.7199 rms_B_bonded: 1.90 r_work: 0.7389 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.7349 rms_B_bonded: 1.18 restraints_weight: 0.2500 r_work: 0.7276 rms_B_bonded: 4.09 restraints_weight: 0.1250 r_work (final): 0.7276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2462 moved from start: 6.9728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.100 1.938 18322 Z= 6.322 Angle : 9.312 100.784 26466 Z= 5.500 Chirality : 0.282 3.274 3060 Planarity : 0.081 0.250 2910 Dihedral : 44.663 168.554 2520 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 493.90 Ramachandran Plot: Outliers : 33.61 % Allowed : 34.66 % Favored : 31.74 % Rotamer: Outliers : 13.40 % Allowed : 36.73 % Favored : 49.87 % Cbeta Deviations : 22.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 55.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.21 (0.09), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.25 (0.07), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.114 0.013 TYR e 39 PHE 0.129 0.013 PHE f 94 HIS 0.038 0.007 HIS M 50 Details of bonding type rmsd/Z covalent geometry : bond 0.09112 / 5.51 (17250) covalent geometry : angle 8.68758 / 5.21 (23250) link_TRANS : bond 0.19524 / 13.16 ( 1072) link_TRANS : angle 12.95848 / 8.73 ( 3216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4380 Ramachandran restraints generated. 2190 Oldfield, 0 Emsley, 2190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 100 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 21 LYS cc_start: 0.3856 (OUTLIER) cc_final: 0.3238 (mttp) REVERT: N 80 LYS cc_start: 0.1696 (OUTLIER) cc_final: 0.1157 (mptt) REVERT: Q 44 THR cc_start: 0.5778 (p) cc_final: 0.5519 (p) REVERT: V 39 TYR cc_start: 0.0024 (OUTLIER) cc_final: -0.0275 (t80) REVERT: 3 80 LYS cc_start: 0.2255 (OUTLIER) cc_final: 0.1981 (ttpt) REVERT: 7 65 ASN cc_start: 0.1248 (OUTLIER) cc_final: 0.0738 (p0) REVERT: A 15 VAL cc_start: -0.0819 (OUTLIER) cc_final: -0.2064 (p) REVERT: A 46 GLU cc_start: 0.1078 (OUTLIER) cc_final: 0.0727 (mm-30) REVERT: A 98 ASP cc_start: 0.5554 (OUTLIER) cc_final: 0.5308 (m-30) REVERT: I 96 LYS cc_start: 0.0685 (OUTLIER) cc_final: 0.0221 (pptt) REVERT: J 37 VAL cc_start: 0.2635 (OUTLIER) cc_final: 0.2141 (t) REVERT: a 15 VAL cc_start: 0.0022 (OUTLIER) cc_final: -0.1312 (m) REVERT: a 46 GLU cc_start: 0.1183 (OUTLIER) cc_final: 0.0571 (pt0) REVERT: a 65 ASN cc_start: -0.0890 (OUTLIER) cc_final: -0.1272 (t0) REVERT: a 79 GLN cc_start: 0.3176 (OUTLIER) cc_final: 0.2753 (tm130) REVERT: b 15 VAL cc_start: 0.0220 (OUTLIER) cc_final: -0.1402 (p) REVERT: e 21 LYS cc_start: 0.2171 (OUTLIER) cc_final: 0.1882 (ttmt) REVERT: i 79 GLN cc_start: 0.5060 (OUTLIER) cc_final: 0.4795 (pt0) REVERT: j 62 GLN cc_start: 0.2191 (OUTLIER) cc_final: 0.1580 (pp30) REVERT: q 23 LYS cc_start: 0.4493 (OUTLIER) cc_final: 0.3918 (ttmm) REVERT: r 96 LYS cc_start: 0.0471 (OUTLIER) cc_final: -0.0276 (tptp) outliers start: 213 outliers final: 145 residues processed: 292 average time/residue: 0.3621 time to fit residues: 126.4170 Evaluate side-chains 257 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 92 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 21 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 55 VAL Chi-restraints excluded: chain N residue 80 LYS Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 80 LYS Chi-restraints excluded: chain R residue 22 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain V residue 15 VAL Chi-restraints excluded: chain V residue 39 TYR Chi-restraints excluded: chain V residue 57 GLU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Y residue 21 LYS Chi-restraints excluded: chain Y residue 39 TYR Chi-restraints excluded: chain Y residue 40 VAL Chi-restraints excluded: chain Y residue 77 VAL Chi-restraints excluded: chain Z residue 59 THR Chi-restraints excluded: chain Z residue 61 GLU Chi-restraints excluded: chain Z residue 63 VAL Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain 2 residue 42 SER Chi-restraints excluded: chain 2 residue 54 THR Chi-restraints excluded: chain 2 residue 77 VAL Chi-restraints excluded: chain 2 residue 79 GLN Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 3 residue 80 LYS Chi-restraints excluded: chain 6 residue 15 VAL Chi-restraints excluded: chain 6 residue 37 VAL Chi-restraints excluded: chain 6 residue 50 HIS Chi-restraints excluded: chain 6 residue 54 THR Chi-restraints excluded: chain 6 residue 57 GLU Chi-restraints excluded: chain 6 residue 58 LYS Chi-restraints excluded: chain 6 residue 66 VAL Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 87 SER Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 49 VAL Chi-restraints excluded: chain 7 residue 52 VAL Chi-restraints excluded: chain 7 residue 64 THR Chi-restraints excluded: chain 7 residue 65 ASN Chi-restraints excluded: chain 7 residue 70 VAL Chi-restraints excluded: chain 7 residue 71 VAL Chi-restraints excluded: chain 7 residue 72 THR Chi-restraints excluded: chain 7 residue 77 VAL Chi-restraints excluded: chain 7 residue 87 SER Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 39 TYR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 21 LYS Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 39 TYR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 82 VAL Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 75 THR Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 79 GLN Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 88 ILE Chi-restraints excluded: chain a residue 92 THR Chi-restraints excluded: chain a residue 95 VAL Chi-restraints excluded: chain b residue 15 VAL Chi-restraints excluded: chain b residue 44 THR Chi-restraints excluded: chain b residue 61 GLU Chi-restraints excluded: chain b residue 70 VAL Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain e residue 21 LYS Chi-restraints excluded: chain e residue 43 LYS Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 94 PHE Chi-restraints excluded: chain f residue 39 TYR Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 43 LYS Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 75 THR Chi-restraints excluded: chain f residue 88 ILE Chi-restraints excluded: chain f residue 94 PHE Chi-restraints excluded: chain i residue 71 VAL Chi-restraints excluded: chain i residue 79 GLN Chi-restraints excluded: chain j residue 37 VAL Chi-restraints excluded: chain j residue 62 GLN Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 79 GLN Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 57 GLU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain n residue 59 THR Chi-restraints excluded: chain n residue 70 VAL Chi-restraints excluded: chain n residue 77 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 23 LYS Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 77 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 49 VAL Chi-restraints excluded: chain r residue 50 HIS Chi-restraints excluded: chain r residue 52 VAL Chi-restraints excluded: chain r residue 55 VAL Chi-restraints excluded: chain r residue 70 VAL Chi-restraints excluded: chain r residue 71 VAL Chi-restraints excluded: chain r residue 72 THR Chi-restraints excluded: chain r residue 96 LYS Chi-restraints excluded: chain u residue 64 THR Chi-restraints excluded: chain u residue 97 LYS Chi-restraints excluded: chain v residue 57 GLU Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain v residue 88 ILE Chi-restraints excluded: chain v residue 97 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 36 optimal weight: 9.9990 chunk 111 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 138 optimal weight: 40.0000 chunk 47 optimal weight: 50.0000 chunk 1 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 206 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 GLN ** U 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 65 ASN ** 7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 24 GLN ** q 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.7201 r_free = 0.7201 target = 0.713891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.7269 r_free = 0.7269 target = 0.692847 restraints weight = 34144.625| |-----------------------------------------------------------------------------| r_work (start): 0.7181 rms_B_bonded: 1.68 r_work: 0.7364 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.7327 rms_B_bonded: 1.17 restraints_weight: 0.2500 r_work: 0.7250 rms_B_bonded: 4.13 restraints_weight: 0.1250 r_work (final): 0.7250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2559 moved from start: 6.9834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.100 1.952 18322 Z= 6.314 Angle : 9.309 100.869 26466 Z= 5.495 Chirality : 0.282 3.176 3060 Planarity : 0.081 0.249 2910 Dihedral : 44.591 168.560 2520 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 498.84 Ramachandran Plot: Outliers : 33.65 % Allowed : 34.79 % Favored : 31.55 % Rotamer: Outliers : 13.40 % Allowed : 36.86 % Favored : 49.75 % Cbeta Deviations : 22.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 55.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -8.20 (0.10), residues: 2190 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.24 (0.07), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.178 0.014 TYR e 39 PHE 0.122 0.013 PHE f 94 HIS 0.037 0.008 HIS f 50 Details of bonding type rmsd/Z covalent geometry : bond 0.09121 / 5.51 (17250) covalent geometry : angle 8.68801 / 5.20 (23250) link_TRANS : bond 0.19469 / 13.12 ( 1072) link_TRANS : angle 12.93954 / 8.72 ( 3216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7532.12 seconds wall clock time: 133 minutes 19.27 seconds (7999.27 seconds total)