Starting phenix.real_space_refine on Sat Aug 23 12:36:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqh_23486/08_2025/7lqh_23486.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqh_23486/08_2025/7lqh_23486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqh_23486/08_2025/7lqh_23486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqh_23486/08_2025/7lqh_23486.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqh_23486/08_2025/7lqh_23486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqh_23486/08_2025/7lqh_23486.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.029 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 8640 2.51 5 N 1584 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 324 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12096 Number of models: 1 Model: "" Number of chains: 144 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "UA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "VA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "WA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "XA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "aA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "cA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "dA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "eA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "fA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "gA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "hA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "iA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "jA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "kA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "lA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "mA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "nA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "oA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "pA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "qA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "rA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "sA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "tA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "uA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "vA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "wA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "xA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "yA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "zA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "i" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "PB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.49, per 1000 atoms: 0.21 Number of scatterers: 12096 At special positions: 0 Unit cell: (89.64, 89.64, 111.24, 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 1872 8.00 N 1584 7.00 C 8640 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=35, symmetry=0 Number of additional bonds: simple=35, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 197.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'M' and resid 1006 through 1007 Processing sheet with id=AA3, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'T' and resid 1006 through 1007 Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'j' and resid 1006 through 1007 Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'q' and resid 1006 through 1007 Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'x' and resid 1006 through 1007 Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AB3, first strand: chain '4' and resid 1006 through 1007 Processing sheet with id=AB4, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AB5, first strand: chain 'BA' and resid 1006 through 1007 Processing sheet with id=AB6, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AB7, first strand: chain 'IA' and resid 1006 through 1007 Processing sheet with id=AB8, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AB9, first strand: chain 'PA' and resid 1006 through 1007 Processing sheet with id=AC1, first strand: chain 'h' and resid 2 through 6 removed outlier: 3.535A pdb=" N PHEGB 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE h 5 " --> pdb=" O PHEGB 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE2A 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE f 5 " --> pdb=" O PHE2A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEoA 105 " --> pdb=" O PHE d 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE d 5 " --> pdb=" O PHEoA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEaA 105 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE b 5 " --> pdb=" O PHEaA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHETA 105 " --> pdb=" O PHE a 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE a 5 " --> pdb=" O PHETA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHEhA 105 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE c 5 " --> pdb=" O PHEhA 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEvA 105 " --> pdb=" O PHE e 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE e 5 " --> pdb=" O PHEvA 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE9A 105 " --> pdb=" O PHE g 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE g 5 " --> pdb=" O PHE9A 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHENB 105 " --> pdb=" O PHE i 3 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE i 5 " --> pdb=" O PHENB 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HB' and resid 202 through 206 removed outlier: 3.521A pdb=" N LYSIB 302 " --> pdb=" O GMA3A 208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS3A 206 " --> pdb=" O GLUIB 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAIB 308 " --> pdb=" O LYS3A 202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS4A 302 " --> pdb=" O GMApA 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYSpA 206 " --> pdb=" O GLU4A 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSqA 302 " --> pdb=" O GMAbA 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSbA 206 " --> pdb=" O GLUqA 304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYScA 302 " --> pdb=" O GMAUA 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSUA 206 " --> pdb=" O GLUcA 304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAcA 308 " --> pdb=" O LYSUA 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSVA 302 " --> pdb=" O GMAiA 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSiA 206 " --> pdb=" O GLUVA 304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAVA 308 " --> pdb=" O LYSiA 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSjA 302 " --> pdb=" O GMAwA 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYSwA 206 " --> pdb=" O GLUjA 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSxA 302 " --> pdb=" O GMAAB 208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSAB 206 " --> pdb=" O GLUxA 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMAxA 308 " --> pdb=" O LYSAB 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSBB 302 " --> pdb=" O GMAOB 208 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYSOB 206 " --> pdb=" O GLUBB 304 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'JB' and resid 1002 through 1006 removed outlier: 3.536A pdb=" N PHEKB1105 " --> pdb=" O PHEJB1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEJB1005 " --> pdb=" O PHEKB1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE6A1105 " --> pdb=" O PHE5A1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE5A1005 " --> pdb=" O PHE6A1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEsA1105 " --> pdb=" O PHErA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHErA1005 " --> pdb=" O PHEsA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEeA1105 " --> pdb=" O PHEdA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEdA1005 " --> pdb=" O PHEeA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEXA1105 " --> pdb=" O PHEWA1003 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHEWA1005 " --> pdb=" O PHEXA1103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHElA1105 " --> pdb=" O PHEkA1003 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHEkA1005 " --> pdb=" O PHElA1103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHEzA1105 " --> pdb=" O PHEyA1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEyA1005 " --> pdb=" O PHEzA1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEDB1105 " --> pdb=" O PHECB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHECB1005 " --> pdb=" O PHEDB1103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHERB1105 " --> pdb=" O PHEQB1003 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHEQB1005 " --> pdb=" O PHERB1103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LB' and resid 1202 through 1206 removed outlier: 3.521A pdb=" N LYSMB1302 " --> pdb=" O GMA7A1208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS7A1206 " --> pdb=" O GLUMB1304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAMB1308 " --> pdb=" O LYS7A1202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS8A1302 " --> pdb=" O GMAtA1208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYStA1206 " --> pdb=" O GLU8A1304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSuA1302 " --> pdb=" O GMAfA1208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYSfA1206 " --> pdb=" O GLUuA1304 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSgA1302 " --> pdb=" O GMAYA1208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSYA1206 " --> pdb=" O GLUgA1304 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GMAgA1308 " --> pdb=" O LYSYA1202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSZA1302 " --> pdb=" O GMAmA1208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSmA1206 " --> pdb=" O GLUZA1304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GMAZA1308 " --> pdb=" O LYSmA1202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSnA1302 " --> pdb=" O GMA0A1208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS0A1206 " --> pdb=" O GLUnA1304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS1A1302 " --> pdb=" O GMAEB1208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSEB1206 " --> pdb=" O GLU1A1304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMA1A1308 " --> pdb=" O LYSEB1202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSFB1302 " --> pdb=" O GMASB1208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSSB1206 " --> pdb=" O GLUFB1304 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 1489 1.26 - 1.33: 1391 1.33 - 1.41: 3600 1.41 - 1.48: 1308 1.48 - 1.56: 4740 Bond restraints: 12528 Sorted by residual: bond pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRrA1001 " pdb=" CAL 5CRrA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" N 5CRyA1001 " pdb=" CAL 5CRyA1001 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 ... (remaining 12523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 14239 1.98 - 3.96: 1589 3.96 - 5.94: 318 5.94 - 7.92: 108 7.92 - 9.90: 18 Bond angle restraints: 16272 Sorted by residual: angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.81 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.80 -9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR5A1001 " pdb=" CAL 5CR5A1001 " pdb=" CAA 5CR5A1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " pdb=" CAA 5CR a 1 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CRWA1001 " pdb=" CAL 5CRWA1001 " pdb=" CAA 5CRWA1001 " ideal model delta sigma weight residual 114.91 124.79 -9.88 3.00e+00 1.11e-01 1.08e+01 ... (remaining 16267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 4844 15.26 - 30.52: 790 30.52 - 45.79: 342 45.79 - 61.05: 198 61.05 - 76.31: 18 Dihedral angle restraints: 6192 sinusoidal: 2880 harmonic: 3312 Sorted by residual: dihedral pdb=" CA LYSMA 106 " pdb=" CB LYSMA 106 " pdb=" CG LYSMA 106 " pdb=" CD LYSMA 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.26 58.74 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYSQA1106 " pdb=" CB LYSQA1106 " pdb=" CG LYSQA1106 " pdb=" CD LYSQA1106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS 1 106 " pdb=" CB LYS 1 106 " pdb=" CG LYS 1 106 " pdb=" CD LYS 1 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.29 58.71 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.018: 407 0.018 - 0.036: 334 0.036 - 0.054: 299 0.054 - 0.073: 89 0.073 - 0.091: 23 Chirality restraints: 1152 Sorted by residual: chirality pdb=" CA LYS R 202 " pdb=" N LYS R 202 " pdb=" C LYS R 202 " pdb=" CB LYS R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.06e-01 chirality pdb=" CA LYS V1202 " pdb=" N LYS V1202 " pdb=" C LYS V1202 " pdb=" CB LYS V1202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 2.02e-01 chirality pdb=" CA LYS Y 202 " pdb=" N LYS Y 202 " pdb=" C LYS Y 202 " pdb=" CB LYS Y 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.86e-01 ... (remaining 1149 not shown) Planarity restraints: 2160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEUA 205 " -0.008 2.00e-02 2.50e+03 7.00e-03 8.57e-01 pdb=" CG PHEUA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEUA 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEUA 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEUA 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEUA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEYA1205 " -0.009 2.00e-02 2.50e+03 6.98e-03 8.53e-01 pdb=" CG PHEYA1205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEYA1205 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEYA1205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEYA1205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEYA1205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEAB 205 " -0.009 2.00e-02 2.50e+03 6.97e-03 8.51e-01 pdb=" CG PHEAB 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEAB 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEAB 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHEAB 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 2157 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 281 2.66 - 3.22: 10092 3.22 - 3.78: 19029 3.78 - 4.34: 28093 4.34 - 4.90: 46315 Nonbonded interactions: 103810 Sorted by model distance: nonbonded pdb=" CD LYS N1102 " pdb=" OE2 GMA 9 208 " model vdw 2.098 2.752 nonbonded pdb=" OE2 GMA Y 208 " pdb=" CD LYS r1102 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS U1102 " pdb=" OE2 GMA v 208 " model vdw 2.116 2.752 nonbonded pdb=" CD LYS k1102 " pdb=" OE2 GMANA 208 " model vdw 2.117 2.752 nonbonded pdb=" CD LYS Q 102 " pdb=" OE2 GMADA1208 " model vdw 2.118 2.752 ... (remaining 103805 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 '0A' selection = chain '1' selection = chain '1A' selection = chain '2' selection = chain '2A' selection = chain '3' selection = chain '3A' selection = chain '4' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '6A' selection = chain '7' selection = chain '7A' selection = chain '8' selection = chain '8A' selection = chain '9' selection = chain '9A' selection = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'RA' selection = chain 'RB' selection = chain 'S' selection = chain 'SA' selection = chain 'SB' selection = chain 'T' selection = chain 'TA' selection = chain 'TB' selection = chain 'U' selection = chain 'UA' selection = chain 'V' selection = chain 'VA' selection = chain 'W' selection = chain 'WA' selection = chain 'X' selection = chain 'XA' selection = chain 'Y' selection = chain 'YA' selection = chain 'Z' selection = chain 'ZA' selection = chain 'a' selection = chain 'aA' selection = chain 'b' selection = chain 'bA' selection = chain 'c' selection = chain 'cA' selection = chain 'd' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'v' selection = chain 'vA' selection = chain 'w' selection = chain 'wA' selection = chain 'x' selection = chain 'xA' selection = chain 'y' selection = chain 'yA' selection = chain 'z' selection = chain 'zA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.150 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.720 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.034 0.786 12563 Z= 3.145 Angle : 1.417 9.902 16272 Z= 0.592 Chirality : 0.035 0.091 1152 Planarity : 0.002 0.009 2160 Dihedral : 20.718 76.311 3888 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 31.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % 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 aren not related in a simple way. whole: -5.94 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEUA 205 Details of bonding type rmsd covalent geometry : bond 0.01603 (12528) covalent geometry : angle 1.41746 (16272) hydrogen bonds : bond 0.31155 ( 278) hydrogen bonds : angle 15.44491 ( 786) Misc. bond : bond 0.57724 ( 35) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 472 time to evaluate : 0.298 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: A 4 GLU cc_start: 0.7369 (mp0) cc_final: 0.6755 (pm20) REVERT: B 4 GLU cc_start: 0.7493 (mp0) cc_final: 0.6748 (pm20) REVERT: S 306 LYS cc_start: 0.8629 (tttt) cc_final: 0.8357 (mttt) REVERT: Y 206 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8180 (ttmm) REVERT: Z 306 LYS cc_start: 0.8563 (tttt) cc_final: 0.8262 (tttt) REVERT: j 1006 LYS cc_start: 0.8500 (mtmt) cc_final: 0.8034 (mtmt) REVERT: m 1306 LYS cc_start: 0.8633 (tttt) cc_final: 0.8339 (mttt) REVERT: o 204 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7064 (mt-10) REVERT: s 1206 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8228 (ttmm) REVERT: t 1306 LYS cc_start: 0.8695 (tttt) cc_final: 0.8441 (mttt) REVERT: v 206 LYS cc_start: 0.8477 (ttmm) cc_final: 0.8231 (ttmm) REVERT: w 304 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7091 (mm-30) REVERT: w 306 LYS cc_start: 0.8689 (tttt) cc_final: 0.8339 (mttt) REVERT: x 1004 GLU cc_start: 0.7152 (mp0) cc_final: 0.6745 (mp0) REVERT: 0 1304 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7144 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8594 (tttt) cc_final: 0.8264 (tttt) REVERT: F 4 GLU cc_start: 0.7397 (mp0) cc_final: 0.6657 (pm20) REVERT: 3 304 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7148 (mm-30) REVERT: 6 1204 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6808 (mt-10) REVERT: 6 1206 LYS cc_start: 0.8567 (ttmm) cc_final: 0.8366 (ttmm) REVERT: 7 1306 LYS cc_start: 0.8772 (tttt) cc_final: 0.8420 (mttt) REVERT: G 4 GLU cc_start: 0.7313 (mp0) cc_final: 0.6485 (pm20) REVERT: 9 204 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6532 (mt-10) REVERT: AA 306 LYS cc_start: 0.8673 (tttt) cc_final: 0.8387 (mttt) REVERT: DA 1204 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7037 (mt-10) REVERT: EA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8431 (mttt) REVERT: HA 306 LYS cc_start: 0.8699 (tttt) cc_final: 0.8363 (mttt) REVERT: LA 1306 LYS cc_start: 0.8705 (tttt) cc_final: 0.8323 (mttt) REVERT: OA 306 LYS cc_start: 0.8570 (tttt) cc_final: 0.8318 (mttt) REVERT: SA 1306 LYS cc_start: 0.8648 (tttt) cc_final: 0.8295 (tttt) REVERT: a 2 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8344 (ttpt) REVERT: TA 104 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7930 (tm-30) REVERT: TA 105 PHE cc_start: 0.9072 (t80) cc_final: 0.8761 (t80) REVERT: UA 202 LYS cc_start: 0.8784 (tttm) cc_final: 0.8340 (ttmm) REVERT: VA 305 PHE cc_start: 0.8549 (t80) cc_final: 0.8266 (t80) REVERT: WA 1003 PHE cc_start: 0.9115 (t80) cc_final: 0.8755 (t80) REVERT: WA 1005 PHE cc_start: 0.8951 (t80) cc_final: 0.8609 (t80) REVERT: WA 1007 PHE cc_start: 0.9301 (t80) cc_final: 0.8997 (t80) REVERT: XA 1103 PHE cc_start: 0.8930 (t80) cc_final: 0.8678 (t80) REVERT: XA 1107 PHE cc_start: 0.8921 (t80) cc_final: 0.8714 (t80) REVERT: YA 1202 LYS cc_start: 0.8788 (tttm) cc_final: 0.8391 (tttm) REVERT: ZA 1304 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8190 (tm-30) REVERT: aA 103 PHE cc_start: 0.9101 (t80) cc_final: 0.8425 (t80) REVERT: aA 106 LYS cc_start: 0.8822 (tttp) cc_final: 0.8564 (tttp) REVERT: bA 202 LYS cc_start: 0.8841 (tttm) cc_final: 0.8397 (ttmm) REVERT: cA 303 PHE cc_start: 0.9015 (t80) cc_final: 0.8654 (t80) REVERT: cA 304 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8429 (tm-30) REVERT: fA 1202 LYS cc_start: 0.8656 (tttm) cc_final: 0.8373 (tttm) REVERT: c 5 PHE cc_start: 0.8932 (t80) cc_final: 0.8452 (t80) REVERT: c 7 PHE cc_start: 0.9209 (t80) cc_final: 0.8995 (t80) REVERT: hA 106 LYS cc_start: 0.8870 (tttp) cc_final: 0.8657 (tttp) REVERT: iA 202 LYS cc_start: 0.8878 (tttm) cc_final: 0.8562 (ttmm) REVERT: jA 306 LYS cc_start: 0.8334 (tptp) cc_final: 0.8046 (tptp) REVERT: kA 1005 PHE cc_start: 0.9077 (t80) cc_final: 0.8703 (t80) REVERT: lA 1103 PHE cc_start: 0.8901 (t80) cc_final: 0.8521 (t80) REVERT: mA 1206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8582 (tttt) REVERT: nA 1305 PHE cc_start: 0.8662 (t80) cc_final: 0.8453 (t80) REVERT: d 3 PHE cc_start: 0.9295 (t80) cc_final: 0.8996 (t80) REVERT: d 5 PHE cc_start: 0.9090 (t80) cc_final: 0.8869 (t80) REVERT: d 7 PHE cc_start: 0.9253 (t80) cc_final: 0.8845 (t80) REVERT: oA 107 PHE cc_start: 0.8813 (t80) cc_final: 0.8347 (t80) REVERT: pA 202 LYS cc_start: 0.8916 (tttm) cc_final: 0.8524 (mmmm) REVERT: pA 206 LYS cc_start: 0.8826 (tttt) cc_final: 0.8593 (tttt) REVERT: qA 305 PHE cc_start: 0.8722 (t80) cc_final: 0.8402 (t80) REVERT: rA 1005 PHE cc_start: 0.8915 (t80) cc_final: 0.8588 (t80) REVERT: sA 1103 PHE cc_start: 0.9020 (t80) cc_final: 0.8784 (t80) REVERT: tA 1206 LYS cc_start: 0.8812 (tttt) cc_final: 0.8431 (tttt) REVERT: vA 106 LYS cc_start: 0.8825 (tttp) cc_final: 0.8561 (tttp) REVERT: wA 202 LYS cc_start: 0.8733 (tttm) cc_final: 0.8401 (mmmm) REVERT: wA 206 LYS cc_start: 0.8797 (tttt) cc_final: 0.8503 (tttt) REVERT: xA 303 PHE cc_start: 0.8927 (t80) cc_final: 0.8677 (t80) REVERT: zA 1106 LYS cc_start: 0.8767 (tttp) cc_final: 0.8557 (tttp) REVERT: 1A 1303 PHE cc_start: 0.8829 (t80) cc_final: 0.8602 (t80) REVERT: 1A 1305 PHE cc_start: 0.8465 (t80) cc_final: 0.8239 (t80) REVERT: 3A 202 LYS cc_start: 0.8922 (tttm) cc_final: 0.8551 (mmmm) REVERT: 3A 206 LYS cc_start: 0.8739 (tttt) cc_final: 0.8527 (tttt) REVERT: 4A 306 LYS cc_start: 0.8459 (tptp) cc_final: 0.8229 (tptp) REVERT: 4A 307 PHE cc_start: 0.8508 (t80) cc_final: 0.8127 (t80) REVERT: 5A 1003 PHE cc_start: 0.9169 (t80) cc_final: 0.8731 (t80) REVERT: 5A 1005 PHE cc_start: 0.9041 (t80) cc_final: 0.8732 (t80) REVERT: 5A 1007 PHE cc_start: 0.9152 (t80) cc_final: 0.8671 (t80) REVERT: 6A 1106 LYS cc_start: 0.8863 (tttp) cc_final: 0.8585 (tttp) REVERT: 7A 1205 PHE cc_start: 0.8502 (t80) cc_final: 0.8271 (t80) REVERT: 7A 1206 LYS cc_start: 0.8695 (tttt) cc_final: 0.8343 (tttm) REVERT: 9A 104 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: 9A 106 LYS cc_start: 0.8906 (tttp) cc_final: 0.8655 (tttm) REVERT: BB 305 PHE cc_start: 0.8766 (t80) cc_final: 0.8355 (t80) REVERT: BB 307 PHE cc_start: 0.8514 (t80) cc_final: 0.8208 (t80) REVERT: CB 1003 PHE cc_start: 0.9123 (t80) cc_final: 0.8740 (t80) REVERT: CB 1005 PHE cc_start: 0.9008 (t80) cc_final: 0.8652 (t80) REVERT: CB 1007 PHE cc_start: 0.9161 (t80) cc_final: 0.8929 (t80) REVERT: DB 1106 LYS cc_start: 0.8792 (tttp) cc_final: 0.8527 (tttp) REVERT: EB 1202 LYS cc_start: 0.8867 (tttm) cc_final: 0.8491 (tttm) REVERT: EB 1206 LYS cc_start: 0.8740 (tttt) cc_final: 0.8538 (tttm) REVERT: FB 1304 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8667 (tm-30) REVERT: GB 103 PHE cc_start: 0.9078 (t80) cc_final: 0.8876 (t80) REVERT: GB 106 LYS cc_start: 0.8643 (tttp) cc_final: 0.8431 (tttm) REVERT: HB 206 LYS cc_start: 0.8809 (tttt) cc_final: 0.8555 (tttm) REVERT: IB 303 PHE cc_start: 0.8906 (t80) cc_final: 0.8678 (t80) REVERT: IB 304 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8429 (tm-30) REVERT: KB 1105 PHE cc_start: 0.8731 (t80) cc_final: 0.8308 (t80) REVERT: KB 1106 LYS cc_start: 0.8655 (tttp) cc_final: 0.8378 (tttp) REVERT: MB 1303 PHE cc_start: 0.8794 (t80) cc_final: 0.8553 (t80) REVERT: i 6 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8467 (ttpt) REVERT: NB 104 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: OB 206 LYS cc_start: 0.8866 (tttt) cc_final: 0.8654 (tttt) REVERT: PB 304 GLU cc_start: 0.8840 (tm-30) cc_final: 0.6113 (pm20) REVERT: PB 305 PHE cc_start: 0.8434 (t80) cc_final: 0.7272 (t80) REVERT: TB 1305 PHE cc_start: 0.8317 (t80) cc_final: 0.8019 (t80) REVERT: TB 1307 PHE cc_start: 0.8067 (t80) cc_final: 0.7620 (t80) outliers start: 126 outliers final: 85 residues processed: 495 average time/residue: 0.1882 time to fit residues: 114.4027 Evaluate side-chains 550 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 460 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 302 LYS Chi-restraints excluded: chain N residue 1102 LYS Chi-restraints excluded: chain N residue 1106 LYS Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain U residue 1102 LYS Chi-restraints excluded: chain U residue 1106 LYS Chi-restraints excluded: chain W residue 1302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 106 LYS Chi-restraints excluded: chain k residue 1102 LYS Chi-restraints excluded: chain k residue 1106 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain p residue 302 LYS Chi-restraints excluded: chain r residue 1102 LYS Chi-restraints excluded: chain r residue 1106 LYS Chi-restraints excluded: chain t residue 1302 LYS Chi-restraints excluded: chain u residue 102 LYS Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain y residue 1102 LYS Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 1 residue 102 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 302 LYS Chi-restraints excluded: chain 5 residue 1102 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain CA residue 1102 LYS Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain FA residue 102 LYS Chi-restraints excluded: chain FA residue 106 LYS Chi-restraints excluded: chain JA residue 1102 LYS Chi-restraints excluded: chain JA residue 1106 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain QA residue 1102 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 104 GLU Chi-restraints excluded: chain WA residue 1002 LYS Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain dA residue 1002 LYS Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain kA residue 1004 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain d residue 6 LYS Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain rA residue 1004 GLU Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain yA residue 1006 LYS Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 5A residue 1006 LYS Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain 9A residue 104 GLU Chi-restraints excluded: chain CB residue 1002 LYS Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain CB residue 1006 LYS Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain JB residue 1006 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.057997 restraints weight = 33409.696| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.26 r_work: 0.2581 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.341 12563 Z= 4.883 Angle : 3.929 32.936 16272 Z= 1.769 Chirality : 0.301 1.035 1152 Planarity : 0.017 0.058 2160 Dihedral : 21.336 111.528 1779 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 100.61 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.76 % Favored : 84.90 % Rotamer: Outliers : 15.16 % Allowed : 18.06 % Favored : 66.78 % Cbeta Deviations : 13.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.69 % 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 aren not related in a simple way. whole: -6.31 (0.19), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.80 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.118 0.018 PHE4A 305 Details of bonding type rmsd covalent geometry : bond 0.10982 (12528) covalent geometry : angle 3.92882 (16272) hydrogen bonds : bond 0.18522 ( 278) hydrogen bonds : angle 9.45492 ( 786) Misc. bond : bond 0.01143 ( 35) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 453 time to evaluate : 0.480 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: A 6 LYS cc_start: 0.9273 (mtmt) cc_final: 0.8909 (mtmt) REVERT: J 106 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9003 (mmmm) REVERT: M 1004 GLU cc_start: 0.8303 (mp0) cc_final: 0.7535 (mp0) REVERT: N 1104 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8235 (mm-30) REVERT: N 1106 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8790 (mmmm) REVERT: B 4 GLU cc_start: 0.8320 (mp0) cc_final: 0.7686 (mp0) REVERT: Q 106 LYS cc_start: 0.9256 (mmmm) cc_final: 0.8959 (mmmm) REVERT: T 1006 LYS cc_start: 0.9227 (mtmt) cc_final: 0.8761 (mtmt) REVERT: U 1104 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8157 (mm-30) REVERT: U 1106 LYS cc_start: 0.9020 (tptm) cc_final: 0.8692 (tptm) REVERT: W 1302 LYS cc_start: 0.9401 (ttpt) cc_final: 0.9029 (mtpp) REVERT: W 1304 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8253 (mm-30) REVERT: C 6 LYS cc_start: 0.9279 (mtmt) cc_final: 0.9055 (mtmt) REVERT: X 106 LYS cc_start: 0.9157 (mmmm) cc_final: 0.8825 (mmmm) REVERT: Y 206 LYS cc_start: 0.9382 (ttmm) cc_final: 0.9175 (mtpp) REVERT: j 1002 LYS cc_start: 0.8708 (tttt) cc_final: 0.8495 (tttp) REVERT: j 1004 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: j 1006 LYS cc_start: 0.9248 (mtmt) cc_final: 0.8942 (mtmt) REVERT: k 1102 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8263 (ttpt) REVERT: k 1104 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8121 (mm-30) REVERT: k 1106 LYS cc_start: 0.9073 (mmmm) cc_final: 0.8813 (mmmm) REVERT: l 1206 LYS cc_start: 0.9279 (ttmm) cc_final: 0.9058 (ttmm) REVERT: D 4 GLU cc_start: 0.8360 (mp0) cc_final: 0.7793 (mp0) REVERT: n 106 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8707 (mmmm) REVERT: o 204 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8170 (mt-10) REVERT: q 1004 GLU cc_start: 0.8662 (mp0) cc_final: 0.8316 (mp0) REVERT: r 1106 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8870 (mmmm) REVERT: s 1204 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8215 (mt-10) REVERT: t 1304 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8110 (mm-30) REVERT: u 102 LYS cc_start: 0.9227 (ttpt) cc_final: 0.8834 (ttpt) REVERT: u 104 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7971 (mm-30) REVERT: u 106 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8703 (mmmm) REVERT: v 202 LYS cc_start: 0.9357 (mtpt) cc_final: 0.9064 (mmmm) REVERT: y 1102 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8896 (ttpt) REVERT: y 1106 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8863 (mmmm) REVERT: F 4 GLU cc_start: 0.8391 (mp0) cc_final: 0.7471 (mp0) REVERT: 1 106 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8895 (mmmm) REVERT: 3 304 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8244 (mm-30) REVERT: 4 1004 GLU cc_start: 0.8293 (mp0) cc_final: 0.8049 (mp0) REVERT: 4 1006 LYS cc_start: 0.9223 (mtmt) cc_final: 0.9013 (ttmt) REVERT: 5 1104 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8104 (mm-30) REVERT: 6 1202 LYS cc_start: 0.9492 (mtpt) cc_final: 0.8937 (mmmm) REVERT: 6 1204 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8132 (mt-10) REVERT: 7 1304 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8080 (mm-30) REVERT: G 4 GLU cc_start: 0.8245 (mp0) cc_final: 0.7426 (mp0) REVERT: G 6 LYS cc_start: 0.9280 (mtmt) cc_final: 0.8999 (mtmt) REVERT: 8 102 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8976 (ttpt) REVERT: 8 104 GLU cc_start: 0.8691 (mm-30) cc_final: 0.7873 (mm-30) REVERT: BA 1006 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8758 (mtmt) REVERT: CA 1104 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8245 (mm-30) REVERT: CA 1106 LYS cc_start: 0.9085 (mmmm) cc_final: 0.8768 (mmmm) REVERT: EA 1304 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8376 (mm-30) REVERT: FA 106 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8732 (mmmm) REVERT: JA 1106 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8742 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9300 (mtpt) cc_final: 0.9023 (pttm) REVERT: KA 1206 LYS cc_start: 0.9139 (ttmm) cc_final: 0.8923 (pptt) REVERT: LA 1304 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7894 (mm-30) REVERT: LA 1306 LYS cc_start: 0.9319 (tttt) cc_final: 0.9085 (tttt) REVERT: I 4 GLU cc_start: 0.8418 (mp0) cc_final: 0.7232 (mp0) REVERT: MA 102 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8736 (mmtm) REVERT: MA 106 LYS cc_start: 0.9176 (mmmm) cc_final: 0.8932 (mmmt) REVERT: PA 1004 GLU cc_start: 0.8467 (mp0) cc_final: 0.7566 (mp0) REVERT: QA 1102 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8808 (mmmt) REVERT: RA 1202 LYS cc_start: 0.9385 (mtpt) cc_final: 0.9058 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8513 (mm-30) REVERT: a 2 LYS cc_start: 0.9204 (tppt) cc_final: 0.8738 (tppt) REVERT: a 4 GLU cc_start: 0.8771 (tp30) cc_final: 0.8460 (tp30) REVERT: TA 106 LYS cc_start: 0.9131 (tttp) cc_final: 0.8823 (ptmm) REVERT: UA 202 LYS cc_start: 0.9411 (tttm) cc_final: 0.9018 (ttmm) REVERT: UA 204 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7901 (tm-30) REVERT: VA 302 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9075 (tptp) REVERT: VA 306 LYS cc_start: 0.9113 (tptp) cc_final: 0.8890 (tptp) REVERT: WA 1004 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8633 (tp30) REVERT: YA 1202 LYS cc_start: 0.9311 (tttm) cc_final: 0.9044 (tttm) REVERT: YA 1204 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8088 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8460 (tm-30) REVERT: aA 106 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8709 (ptmm) REVERT: bA 202 LYS cc_start: 0.9378 (tttm) cc_final: 0.8941 (ttmm) REVERT: bA 204 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7949 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9229 (ttmt) cc_final: 0.9018 (ttmt) REVERT: dA 1004 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8105 (tp30) REVERT: iA 202 LYS cc_start: 0.9392 (tttm) cc_final: 0.9021 (tppp) REVERT: lA 1103 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.9072 (t80) REVERT: d 2 LYS cc_start: 0.9129 (tppt) cc_final: 0.8583 (tppt) REVERT: d 4 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8248 (tp30) REVERT: pA 202 LYS cc_start: 0.9410 (tttm) cc_final: 0.9187 (tttm) REVERT: pA 204 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7599 (tm-30) REVERT: qA 306 LYS cc_start: 0.9094 (tptp) cc_final: 0.8853 (tptp) REVERT: rA 1002 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9103 (ttpt) REVERT: sA 1103 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8912 (t80) REVERT: tA 1204 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7927 (tm-30) REVERT: e 4 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8464 (tp30) REVERT: vA 104 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8623 (tm-30) REVERT: wA 202 LYS cc_start: 0.9338 (tttm) cc_final: 0.8867 (tppp) REVERT: wA 204 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8192 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9000 (tppt) REVERT: yA 1004 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8396 (tp30) REVERT: 1A 1304 GLU cc_start: 0.9335 (tm-30) cc_final: 0.7884 (tm-30) REVERT: f 2 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8872 (ttmt) REVERT: f 4 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8493 (tp30) REVERT: 3A 202 LYS cc_start: 0.9404 (tttm) cc_final: 0.9058 (ttmm) REVERT: 3A 204 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7844 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8800 (tptp) REVERT: 4A 304 GLU cc_start: 0.9326 (tm-30) cc_final: 0.8267 (tm-30) REVERT: 4A 306 LYS cc_start: 0.9042 (tptp) cc_final: 0.8832 (tptp) REVERT: 5A 1002 LYS cc_start: 0.9244 (ptpt) cc_final: 0.9013 (ptpt) REVERT: 7A 1204 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7885 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8800 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8235 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.8800 (tptp) cc_final: 0.8490 (tptp) REVERT: g 2 LYS cc_start: 0.9185 (tppt) cc_final: 0.8676 (tppt) REVERT: g 4 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8459 (tp30) REVERT: 9A 105 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.9105 (t80) REVERT: AB 202 LYS cc_start: 0.9341 (tttm) cc_final: 0.8959 (ttmm) REVERT: AB 204 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8067 (tm-30) REVERT: BB 302 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8964 (tptp) REVERT: BB 306 LYS cc_start: 0.9062 (tptp) cc_final: 0.8858 (tptp) REVERT: CB 1004 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8440 (tp30) REVERT: DB 1102 LYS cc_start: 0.9258 (tptm) cc_final: 0.9043 (tptm) REVERT: EB 1204 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7488 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9011 (tptp) cc_final: 0.8779 (tptp) REVERT: FB 1303 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8360 (t80) REVERT: FB 1306 LYS cc_start: 0.9001 (tptp) cc_final: 0.8793 (tptp) REVERT: HB 202 LYS cc_start: 0.9408 (tttm) cc_final: 0.8962 (pttm) REVERT: IB 306 LYS cc_start: 0.9035 (tptp) cc_final: 0.8790 (tptp) REVERT: IB 307 PHE cc_start: 0.9381 (t80) cc_final: 0.9147 (t80) REVERT: JB 1004 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8190 (tp30) REVERT: LB 1202 LYS cc_start: 0.9329 (tttm) cc_final: 0.9019 (pptt) REVERT: i 4 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: NB 102 LYS cc_start: 0.9346 (tptm) cc_final: 0.9118 (pttt) REVERT: NB 103 PHE cc_start: 0.9116 (t80) cc_final: 0.8776 (t80) REVERT: NB 104 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8300 (pm20) REVERT: OB 202 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9132 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8230 (tp30) REVERT: QB 1006 LYS cc_start: 0.9264 (ttpt) cc_final: 0.8946 (ttpt) REVERT: SB 1204 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8270 (tm-30) outliers start: 131 outliers final: 67 residues processed: 497 average time/residue: 0.1989 time to fit residues: 121.0763 Evaluate side-chains 549 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 453 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain MA residue 102 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain rA residue 1002 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.059105 restraints weight = 33958.379| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.25 r_work: 0.2616 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.7067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.338 12563 Z= 4.888 Angle : 4.002 34.612 16272 Z= 1.803 Chirality : 0.299 1.003 1152 Planarity : 0.017 0.057 2160 Dihedral : 20.681 89.761 1519 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 106.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 18.06 % Favored : 81.77 % Rotamer: Outliers : 20.95 % Allowed : 21.88 % Favored : 57.18 % Cbeta Deviations : 14.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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 aren not related in a simple way. whole: -5.73 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.123 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11005 (12528) covalent geometry : angle 4.00180 (16272) hydrogen bonds : bond 0.18772 ( 278) hydrogen bonds : angle 9.39435 ( 786) Misc. bond : bond 0.01217 ( 35) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 438 time to evaluate : 0.460 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: A 6 LYS cc_start: 0.9260 (mtmt) cc_final: 0.9009 (mtmt) REVERT: K 206 LYS cc_start: 0.9298 (ttmm) cc_final: 0.9091 (ttmm) REVERT: M 1004 GLU cc_start: 0.8367 (mp0) cc_final: 0.7579 (mp0) REVERT: N 1104 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8339 (mm-30) REVERT: N 1106 LYS cc_start: 0.9168 (mmmm) cc_final: 0.8794 (mmmm) REVERT: P 1304 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8744 (mm-30) REVERT: B 4 GLU cc_start: 0.8400 (mp0) cc_final: 0.7919 (mp0) REVERT: Q 106 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8935 (mmmm) REVERT: S 307 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9069 (m-80) REVERT: T 1004 GLU cc_start: 0.8700 (mp0) cc_final: 0.8027 (mp0) REVERT: T 1006 LYS cc_start: 0.9321 (mtmt) cc_final: 0.9042 (mtmt) REVERT: U 1104 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8088 (mm-30) REVERT: U 1106 LYS cc_start: 0.9096 (tptm) cc_final: 0.8617 (tptm) REVERT: C 4 GLU cc_start: 0.8461 (mp0) cc_final: 0.7952 (mp0) REVERT: X 106 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8871 (mmmm) REVERT: Z 304 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8796 (mm-30) REVERT: j 1002 LYS cc_start: 0.8702 (tttt) cc_final: 0.8425 (tttp) REVERT: j 1004 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: j 1006 LYS cc_start: 0.9262 (mtmt) cc_final: 0.8950 (mtmt) REVERT: k 1102 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8191 (ttpt) REVERT: k 1104 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8269 (mm-30) REVERT: k 1106 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8722 (mmmm) REVERT: l 1202 LYS cc_start: 0.9364 (mtpt) cc_final: 0.9139 (mtpp) REVERT: l 1204 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8708 (mm-30) REVERT: l 1206 LYS cc_start: 0.9335 (ttmm) cc_final: 0.9101 (ttmm) REVERT: D 4 GLU cc_start: 0.8384 (mp0) cc_final: 0.7847 (mp0) REVERT: n 106 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8752 (mmmm) REVERT: o 202 LYS cc_start: 0.9399 (ttpt) cc_final: 0.9191 (ttpt) REVERT: o 204 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8407 (mt-10) REVERT: q 1004 GLU cc_start: 0.8606 (mp0) cc_final: 0.8234 (mp0) REVERT: r 1104 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8004 (mm-30) REVERT: r 1106 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8853 (mmmm) REVERT: s 1204 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8466 (mt-10) REVERT: t 1304 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8266 (mm-30) REVERT: E 6 LYS cc_start: 0.9214 (mtmt) cc_final: 0.8960 (mtmt) REVERT: u 106 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8688 (mmmm) REVERT: v 206 LYS cc_start: 0.9418 (ttmm) cc_final: 0.9215 (ttmm) REVERT: w 307 PHE cc_start: 0.9535 (OUTLIER) cc_final: 0.9056 (m-80) REVERT: x 1003 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.8172 (m-80) REVERT: y 1102 LYS cc_start: 0.9221 (ttpt) cc_final: 0.8875 (ttpt) REVERT: y 1106 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8901 (mmmm) REVERT: 1 106 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8653 (mmmm) REVERT: 3 304 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8543 (mm-30) REVERT: 4 1004 GLU cc_start: 0.8374 (mp0) cc_final: 0.8100 (mp0) REVERT: 4 1006 LYS cc_start: 0.9157 (mtmt) cc_final: 0.8957 (ttmt) REVERT: 6 1202 LYS cc_start: 0.9503 (mtpt) cc_final: 0.9090 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8437 (mm-30) REVERT: G 4 GLU cc_start: 0.8318 (mp0) cc_final: 0.7751 (mp0) REVERT: G 6 LYS cc_start: 0.9278 (mtmt) cc_final: 0.9060 (mtmt) REVERT: 8 106 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8699 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8360 (mp0) cc_final: 0.8111 (mp0) REVERT: FA 104 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8032 (mm-30) REVERT: FA 106 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8831 (mmmm) REVERT: HA 302 LYS cc_start: 0.9360 (mtpt) cc_final: 0.9043 (mtpp) REVERT: JA 1106 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8704 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9275 (mtpt) cc_final: 0.9022 (pttm) REVERT: I 4 GLU cc_start: 0.8247 (mp0) cc_final: 0.7861 (mp0) REVERT: I 6 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9032 (ttmt) REVERT: MA 102 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8849 (mmtt) REVERT: PA 1004 GLU cc_start: 0.8339 (mp0) cc_final: 0.7544 (mp0) REVERT: QA 1106 LYS cc_start: 0.6296 (tptt) cc_final: 0.5583 (tptp) REVERT: RA 1202 LYS cc_start: 0.9326 (mtpt) cc_final: 0.9034 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8651 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: a 2 LYS cc_start: 0.9213 (tppt) cc_final: 0.8836 (tppt) REVERT: a 4 GLU cc_start: 0.8818 (tp30) cc_final: 0.8509 (tp30) REVERT: TA 106 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8843 (ptmm) REVERT: VA 302 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8913 (tptp) REVERT: VA 306 LYS cc_start: 0.9091 (tptp) cc_final: 0.8824 (tptp) REVERT: WA 1002 LYS cc_start: 0.9247 (tppt) cc_final: 0.8874 (tppt) REVERT: WA 1004 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8629 (tp30) REVERT: XA 1105 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8776 (p90) REVERT: YA 1202 LYS cc_start: 0.9373 (tttm) cc_final: 0.9136 (tttm) REVERT: YA 1204 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7850 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8759 (t80) REVERT: ZA 1304 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8486 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8867 (tptp) cc_final: 0.8627 (tptp) REVERT: bA 202 LYS cc_start: 0.9343 (tttm) cc_final: 0.8970 (ttmm) REVERT: dA 1002 LYS cc_start: 0.9236 (ttmt) cc_final: 0.9016 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9201 (tm-30) cc_final: 0.7953 (tm-30) REVERT: iA 202 LYS cc_start: 0.9431 (tttm) cc_final: 0.9009 (tppp) REVERT: iA 204 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7970 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.9091 (t80) REVERT: nA 1306 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8853 (tptp) REVERT: d 4 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8052 (tp30) REVERT: oA 102 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9041 (tptm) REVERT: pA 204 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7623 (tm-30) REVERT: qA 306 LYS cc_start: 0.9071 (tptp) cc_final: 0.8797 (tptp) REVERT: rA 1006 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8833 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7788 (tm-30) REVERT: e 4 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8378 (tp30) REVERT: e 6 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8763 (ttpt) REVERT: wA 202 LYS cc_start: 0.9327 (tttm) cc_final: 0.8834 (tppp) REVERT: wA 204 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8159 (tm-30) REVERT: yA 1002 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8846 (tppt) REVERT: yA 1004 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: zA 1102 LYS cc_start: 0.9385 (tptm) cc_final: 0.9159 (tptm) REVERT: 1A 1304 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8176 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8952 (t80) REVERT: f 2 LYS cc_start: 0.9223 (ttmt) cc_final: 0.8862 (ttmt) REVERT: f 4 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8486 (tp30) REVERT: 3A 202 LYS cc_start: 0.9368 (tttm) cc_final: 0.9012 (ttmm) REVERT: 3A 204 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7944 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8839 (tptp) REVERT: 4A 304 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8318 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8428 (tm-30) cc_final: 0.7967 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8864 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8167 (tm-30) REVERT: g 2 LYS cc_start: 0.9135 (tppt) cc_final: 0.8620 (tppt) REVERT: g 4 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8371 (tp30) REVERT: 9A 105 PHE cc_start: 0.9455 (OUTLIER) cc_final: 0.9160 (t80) REVERT: AB 202 LYS cc_start: 0.9389 (tttm) cc_final: 0.8994 (ttmm) REVERT: AB 204 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7986 (tm-30) REVERT: BB 302 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8990 (tptp) REVERT: CB 1004 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8496 (tp30) REVERT: EB 1204 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7420 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8660 (tptp) REVERT: FB 1306 LYS cc_start: 0.8976 (tptp) cc_final: 0.8727 (tptp) REVERT: h 4 GLU cc_start: 0.8725 (tp30) cc_final: 0.7889 (pm20) REVERT: HB 202 LYS cc_start: 0.9355 (tttm) cc_final: 0.8957 (pttt) REVERT: JB 1004 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: i 4 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: NB 102 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9099 (pttt) REVERT: NB 104 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: NB 105 PHE cc_start: 0.9091 (t80) cc_final: 0.8887 (t80) REVERT: NB 106 LYS cc_start: 0.9244 (tttp) cc_final: 0.8718 (pptt) REVERT: OB 202 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9172 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8154 (tp30) REVERT: RB 1103 PHE cc_start: 0.9032 (t80) cc_final: 0.8611 (t80) REVERT: SB 1204 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8313 (tm-30) outliers start: 181 outliers final: 111 residues processed: 509 average time/residue: 0.2192 time to fit residues: 136.7565 Evaluate side-chains 586 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 437 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1206 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain 8 residue 106 LYS Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1002 LYS Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1003 PHE Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain NB residue 104 GLU Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.070752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.059893 restraints weight = 33709.132| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.24 r_work: 0.2634 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.7390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.366 12563 Z= 4.891 Angle : 4.040 32.405 16272 Z= 1.828 Chirality : 0.299 0.979 1152 Planarity : 0.017 0.058 2160 Dihedral : 20.740 81.956 1507 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 107.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 18.58 % Favored : 81.25 % Rotamer: Outliers : 24.42 % Allowed : 21.30 % Favored : 54.28 % Cbeta Deviations : 14.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.39 % 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 aren not related in a simple way. whole: -5.91 (0.23), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.49 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11018 (12528) covalent geometry : angle 4.03969 (16272) hydrogen bonds : bond 0.18915 ( 278) hydrogen bonds : angle 9.37443 ( 786) Misc. bond : bond 0.01195 ( 35) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 433 time to evaluate : 0.725 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: A 4 GLU cc_start: 0.7983 (mp0) cc_final: 0.7356 (mp0) REVERT: M 1004 GLU cc_start: 0.8415 (mp0) cc_final: 0.7604 (mp0) REVERT: N 1104 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8414 (mm-30) REVERT: N 1106 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8660 (mmmm) REVERT: P 1304 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8752 (mm-30) REVERT: B 4 GLU cc_start: 0.8387 (mp0) cc_final: 0.7936 (mp0) REVERT: S 307 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9041 (m-80) REVERT: T 1004 GLU cc_start: 0.8680 (mp0) cc_final: 0.7975 (mp0) REVERT: T 1006 LYS cc_start: 0.9310 (mtmt) cc_final: 0.9080 (mtmt) REVERT: U 1104 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8145 (mm-30) REVERT: U 1106 LYS cc_start: 0.9078 (tptm) cc_final: 0.8671 (tptm) REVERT: W 1302 LYS cc_start: 0.9405 (mtpt) cc_final: 0.9065 (mtpp) REVERT: W 1304 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8524 (mm-30) REVERT: C 4 GLU cc_start: 0.8477 (mp0) cc_final: 0.8057 (mp0) REVERT: X 106 LYS cc_start: 0.9307 (mmmm) cc_final: 0.8969 (mmmm) REVERT: Z 304 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8757 (mm-30) REVERT: j 1004 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: j 1006 LYS cc_start: 0.9260 (mtmt) cc_final: 0.8843 (mtmt) REVERT: k 1102 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8499 (ttpt) REVERT: k 1104 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8266 (mm-30) REVERT: k 1106 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8753 (mmmm) REVERT: l 1202 LYS cc_start: 0.9379 (mtpt) cc_final: 0.9105 (mtpp) REVERT: l 1204 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8616 (mm-30) REVERT: D 4 GLU cc_start: 0.8363 (mp0) cc_final: 0.7693 (mp0) REVERT: D 6 LYS cc_start: 0.9202 (mtmt) cc_final: 0.8708 (mtmt) REVERT: D 7 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8690 (t80) REVERT: n 106 LYS cc_start: 0.9203 (mmmm) cc_final: 0.8711 (mmmm) REVERT: o 202 LYS cc_start: 0.9421 (ttpt) cc_final: 0.9147 (ttpt) REVERT: q 1004 GLU cc_start: 0.8495 (mp0) cc_final: 0.8134 (mp0) REVERT: r 1104 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7962 (mm-30) REVERT: r 1106 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8820 (mmmm) REVERT: s 1204 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8500 (mt-10) REVERT: E 6 LYS cc_start: 0.9214 (mtmt) cc_final: 0.8908 (mtmt) REVERT: u 106 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8553 (mmmm) REVERT: v 206 LYS cc_start: 0.9439 (ttmm) cc_final: 0.9231 (ttmm) REVERT: x 1003 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: x 1006 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8649 (mtmt) REVERT: y 1102 LYS cc_start: 0.9181 (ttpt) cc_final: 0.8834 (ttpt) REVERT: y 1106 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8867 (mmmm) REVERT: 1 104 GLU cc_start: 0.8586 (mm-30) cc_final: 0.7976 (mm-30) REVERT: 1 106 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8644 (mmmm) REVERT: 3 302 LYS cc_start: 0.9443 (ttpt) cc_final: 0.9028 (ttmm) REVERT: 5 1104 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8041 (mm-30) REVERT: 5 1106 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8879 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9487 (mtpt) cc_final: 0.9080 (mtpp) REVERT: 7 1304 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8387 (mm-30) REVERT: G 3 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: G 4 GLU cc_start: 0.8348 (mp0) cc_final: 0.7974 (mp0) REVERT: G 6 LYS cc_start: 0.9279 (mtmt) cc_final: 0.9060 (mtmt) REVERT: 8 104 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7906 (mm-30) REVERT: 8 106 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8535 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8565 (mp0) cc_final: 0.8122 (mp0) REVERT: CA 1106 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8785 (mmmm) REVERT: H 4 GLU cc_start: 0.4419 (OUTLIER) cc_final: 0.3028 (pm20) REVERT: FA 104 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8139 (mm-30) REVERT: FA 106 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8892 (mmmm) REVERT: GA 207 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8936 (t80) REVERT: HA 302 LYS cc_start: 0.9352 (mtpt) cc_final: 0.9017 (mtpp) REVERT: HA 304 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8551 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8732 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9268 (mtpt) cc_final: 0.9000 (pttm) REVERT: KA 1204 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5985 (pm20) REVERT: I 4 GLU cc_start: 0.8246 (mp0) cc_final: 0.7301 (mp0) REVERT: I 6 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8986 (mtmt) REVERT: MA 106 LYS cc_start: 0.4943 (OUTLIER) cc_final: 0.4518 (tptp) REVERT: NA 202 LYS cc_start: 0.9429 (mtpt) cc_final: 0.8972 (mptt) REVERT: PA 1004 GLU cc_start: 0.8459 (mp0) cc_final: 0.8184 (mp0) REVERT: QA 1106 LYS cc_start: 0.5043 (OUTLIER) cc_final: 0.2104 (mmmt) REVERT: RA 1202 LYS cc_start: 0.9323 (mtpt) cc_final: 0.9070 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8639 (mm-30) REVERT: SA 1307 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.8760 (m-80) REVERT: a 2 LYS cc_start: 0.9239 (tppt) cc_final: 0.8941 (tppt) REVERT: a 4 GLU cc_start: 0.8829 (tp30) cc_final: 0.8528 (tp30) REVERT: TA 106 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8870 (ptmm) REVERT: UA 204 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7795 (tm-30) REVERT: VA 302 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9060 (tptp) REVERT: WA 1002 LYS cc_start: 0.9245 (tppt) cc_final: 0.8877 (tppt) REVERT: WA 1004 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8669 (tp30) REVERT: XA 1105 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8786 (p90) REVERT: YA 1204 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7850 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9186 (OUTLIER) cc_final: 0.8833 (t80) REVERT: ZA 1304 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8535 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8933 (tptp) cc_final: 0.8675 (tptp) REVERT: bA 202 LYS cc_start: 0.9351 (tttm) cc_final: 0.9004 (ttmm) REVERT: bA 204 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8145 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9245 (ttmt) cc_final: 0.9017 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9233 (tm-30) cc_final: 0.7894 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9290 (t80) cc_final: 0.8936 (t80) REVERT: c 4 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: iA 202 LYS cc_start: 0.9450 (tttm) cc_final: 0.9024 (tppp) REVERT: iA 204 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7942 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.9105 (t80) REVERT: nA 1306 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8907 (tptp) REVERT: d 4 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8089 (tp30) REVERT: oA 102 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9066 (tptm) REVERT: pA 204 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7553 (tm-30) REVERT: qA 306 LYS cc_start: 0.9070 (tptp) cc_final: 0.8800 (tptp) REVERT: rA 1006 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8822 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8647 (tm-30) cc_final: 0.7908 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9177 (tttt) cc_final: 0.8970 (tmtt) REVERT: uA 1307 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.9068 (t80) REVERT: e 4 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8386 (tp30) REVERT: e 6 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8806 (ttpt) REVERT: vA 104 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8574 (tm-30) REVERT: wA 202 LYS cc_start: 0.9326 (tttm) cc_final: 0.8960 (ttmm) REVERT: wA 204 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8210 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: zA 1102 LYS cc_start: 0.9393 (tptm) cc_final: 0.9179 (tptm) REVERT: 1A 1304 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8484 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.9034 (t80) REVERT: f 2 LYS cc_start: 0.9216 (ttmt) cc_final: 0.8847 (ttmt) REVERT: f 4 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8483 (tp30) REVERT: 3A 202 LYS cc_start: 0.9353 (tttm) cc_final: 0.9044 (mmmm) REVERT: 4A 304 GLU cc_start: 0.9290 (tm-30) cc_final: 0.8300 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7967 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8908 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8259 (tm-30) REVERT: g 2 LYS cc_start: 0.9166 (tppt) cc_final: 0.8632 (tppt) REVERT: g 4 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8332 (tp30) REVERT: 9A 105 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.9193 (t80) REVERT: AB 202 LYS cc_start: 0.9430 (tttm) cc_final: 0.9060 (ttmm) REVERT: AB 204 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7995 (tm-30) REVERT: BB 302 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.9027 (tptp) REVERT: BB 305 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.9167 (t80) REVERT: CB 1004 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8486 (tp30) REVERT: DB 1102 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9083 (tptm) REVERT: EB 1204 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7450 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8694 (tptp) REVERT: h 4 GLU cc_start: 0.8715 (tp30) cc_final: 0.8083 (pm20) REVERT: GB 103 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.9117 (t80) REVERT: HB 202 LYS cc_start: 0.9399 (tttm) cc_final: 0.9031 (pttt) REVERT: IB 306 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8871 (tptp) REVERT: JB 1004 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8239 (tp30) REVERT: LB 1202 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9107 (pptt) REVERT: MB 1306 LYS cc_start: 0.9040 (tptp) cc_final: 0.8810 (tptp) REVERT: i 4 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8430 (tp30) REVERT: NB 102 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9097 (pttt) REVERT: NB 104 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8289 (pm20) REVERT: NB 106 LYS cc_start: 0.9223 (tttp) cc_final: 0.8698 (pptt) REVERT: OB 202 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9178 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8034 (tp30) REVERT: QB 1005 PHE cc_start: 0.9276 (t80) cc_final: 0.8646 (t80) outliers start: 211 outliers final: 130 residues processed: 516 average time/residue: 0.2204 time to fit residues: 139.8915 Evaluate side-chains 611 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 432 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 4 residue 1002 LYS Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain AA residue 304 GLU Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1206 LYS Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain QA residue 1104 GLU Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 105 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.060014 restraints weight = 34726.623| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.22 r_work: 0.2644 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.7510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.345 12563 Z= 4.895 Angle : 4.051 30.089 16272 Z= 1.833 Chirality : 0.299 0.972 1152 Planarity : 0.017 0.057 2160 Dihedral : 20.621 82.061 1496 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 107.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.44 % Favored : 80.38 % Rotamer: Outliers : 25.46 % Allowed : 22.69 % Favored : 51.85 % Cbeta Deviations : 14.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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 aren not related in a simple way. whole: -5.93 (0.23), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11025 (12528) covalent geometry : angle 4.05106 (16272) hydrogen bonds : bond 0.19057 ( 278) hydrogen bonds : angle 9.46096 ( 786) Misc. bond : bond 0.01141 ( 35) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 431 time to evaluate : 0.485 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: A 6 LYS cc_start: 0.9297 (mtmt) cc_final: 0.9011 (mtmt) REVERT: M 1004 GLU cc_start: 0.8495 (mp0) cc_final: 0.7716 (mp0) REVERT: N 1104 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8559 (mm-30) REVERT: N 1106 LYS cc_start: 0.9123 (mmmm) cc_final: 0.8677 (mmmm) REVERT: O 1206 LYS cc_start: 0.9264 (ttmm) cc_final: 0.9051 (ttmm) REVERT: B 4 GLU cc_start: 0.8405 (mp0) cc_final: 0.8064 (mp0) REVERT: B 5 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.9189 (m-80) REVERT: Q 104 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8147 (mm-30) REVERT: Q 106 LYS cc_start: 0.9292 (mmmm) cc_final: 0.8947 (mmmm) REVERT: S 307 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: T 1004 GLU cc_start: 0.8693 (mp0) cc_final: 0.7952 (mp0) REVERT: T 1006 LYS cc_start: 0.9339 (mtmt) cc_final: 0.9061 (mtmt) REVERT: U 1104 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8206 (mm-30) REVERT: U 1106 LYS cc_start: 0.9058 (tptm) cc_final: 0.8655 (tptm) REVERT: W 1302 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9018 (ttmm) REVERT: C 4 GLU cc_start: 0.8541 (mp0) cc_final: 0.8175 (mp0) REVERT: X 106 LYS cc_start: 0.9297 (mmmm) cc_final: 0.8980 (mmmm) REVERT: j 1004 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: j 1006 LYS cc_start: 0.9283 (mtmt) cc_final: 0.8906 (mtmt) REVERT: k 1102 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8220 (ttpt) REVERT: k 1104 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8264 (mm-30) REVERT: k 1106 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8809 (mmmm) REVERT: l 1202 LYS cc_start: 0.9388 (mtpt) cc_final: 0.9125 (mtpp) REVERT: l 1204 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8808 (mm-30) REVERT: D 4 GLU cc_start: 0.8379 (mp0) cc_final: 0.7597 (mp0) REVERT: D 6 LYS cc_start: 0.9297 (mtmt) cc_final: 0.8848 (mtmt) REVERT: D 7 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.8783 (t80) REVERT: n 106 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8760 (mmmm) REVERT: q 1004 GLU cc_start: 0.8560 (mp0) cc_final: 0.8284 (mp0) REVERT: r 1104 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8003 (mm-30) REVERT: r 1106 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8831 (mmmm) REVERT: E 6 LYS cc_start: 0.9218 (mtmt) cc_final: 0.8931 (mtmt) REVERT: u 106 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8532 (mmmm) REVERT: v 206 LYS cc_start: 0.9438 (ttmm) cc_final: 0.9195 (ttmm) REVERT: w 307 PHE cc_start: 0.9545 (OUTLIER) cc_final: 0.8776 (m-80) REVERT: x 1003 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8513 (m-80) REVERT: x 1006 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8741 (mtmt) REVERT: y 1106 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8950 (mmmm) REVERT: F 6 LYS cc_start: 0.9258 (mtmt) cc_final: 0.8931 (mtmt) REVERT: 1 104 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8099 (mm-30) REVERT: 1 106 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8724 (mmmm) REVERT: 5 1106 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8758 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9438 (mtpt) cc_final: 0.9072 (mtpp) REVERT: G 3 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: G 4 GLU cc_start: 0.8341 (mp0) cc_final: 0.7932 (mp0) REVERT: G 6 LYS cc_start: 0.9357 (mtmt) cc_final: 0.9109 (mtmt) REVERT: 8 104 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7900 (mm-30) REVERT: 8 106 LYS cc_start: 0.9095 (mmmm) cc_final: 0.8645 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8466 (mp0) cc_final: 0.7810 (mp0) REVERT: CA 1104 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8207 (mm-30) REVERT: H 4 GLU cc_start: 0.4271 (OUTLIER) cc_final: 0.2888 (pm20) REVERT: FA 106 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8944 (mmmm) REVERT: HA 302 LYS cc_start: 0.9355 (mtpt) cc_final: 0.9034 (mmmm) REVERT: HA 304 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8605 (mm-30) REVERT: JA 1106 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8777 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9257 (mtpt) cc_final: 0.9037 (pttm) REVERT: I 4 GLU cc_start: 0.8253 (mp0) cc_final: 0.7368 (mp0) REVERT: PA 1004 GLU cc_start: 0.8447 (mp0) cc_final: 0.7830 (mp0) REVERT: PA 1006 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9031 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9123 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8565 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9272 (tttt) cc_final: 0.8877 (tttt) REVERT: SA 1307 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.8541 (m-80) REVERT: a 2 LYS cc_start: 0.9300 (tppt) cc_final: 0.9043 (tppt) REVERT: a 4 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8445 (tp30) REVERT: TA 104 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8519 (tm-30) REVERT: TA 106 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8896 (ptmm) REVERT: UA 204 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7849 (tm-30) REVERT: VA 302 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9091 (tptp) REVERT: WA 1002 LYS cc_start: 0.9278 (tppt) cc_final: 0.8903 (tppt) REVERT: WA 1004 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8631 (tp30) REVERT: YA 1204 GLU cc_start: 0.8429 (tm-30) cc_final: 0.7882 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8823 (t80) REVERT: ZA 1304 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8601 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8978 (tptp) cc_final: 0.8758 (tptp) REVERT: aA 104 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8026 (tm-30) REVERT: bA 202 LYS cc_start: 0.9368 (tttm) cc_final: 0.9013 (ttmm) REVERT: bA 204 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8124 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8963 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9235 (tm-30) cc_final: 0.7855 (tm-30) REVERT: c 4 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8375 (tp30) REVERT: iA 204 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8092 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.9115 (t80) REVERT: mA 1206 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8957 (tmtt) REVERT: nA 1306 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8927 (tptp) REVERT: d 4 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: oA 102 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9078 (tptm) REVERT: pA 204 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7657 (tm-30) REVERT: qA 306 LYS cc_start: 0.9131 (tptp) cc_final: 0.8859 (tptp) REVERT: tA 1204 GLU cc_start: 0.8696 (tm-30) cc_final: 0.7932 (tm-30) REVERT: e 4 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8425 (tp30) REVERT: e 6 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8814 (ttpt) REVERT: vA 104 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8598 (tm-30) REVERT: wA 202 LYS cc_start: 0.9336 (tttm) cc_final: 0.8960 (ttmm) REVERT: wA 204 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8260 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8362 (tp30) REVERT: zA 1102 LYS cc_start: 0.9384 (tptm) cc_final: 0.9181 (tptm) REVERT: 1A 1304 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8527 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.9037 (t80) REVERT: f 2 LYS cc_start: 0.9260 (ttmt) cc_final: 0.8910 (ttmt) REVERT: f 4 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: 3A 202 LYS cc_start: 0.9375 (tttm) cc_final: 0.9100 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8206 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8888 (tptp) REVERT: 4A 304 GLU cc_start: 0.9336 (tm-30) cc_final: 0.8422 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8056 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8943 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8325 (tm-30) REVERT: g 2 LYS cc_start: 0.9187 (tppt) cc_final: 0.8681 (tppt) REVERT: g 4 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: AB 202 LYS cc_start: 0.9453 (tttm) cc_final: 0.9103 (ttmm) REVERT: AB 204 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8048 (tm-30) REVERT: BB 302 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9054 (tptp) REVERT: CB 1004 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8439 (tp30) REVERT: DB 1102 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9074 (tptm) REVERT: EB 1204 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7559 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8737 (tptp) REVERT: h 4 GLU cc_start: 0.8816 (tp30) cc_final: 0.8048 (pm20) REVERT: GB 103 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.9148 (t80) REVERT: HB 202 LYS cc_start: 0.9420 (tttm) cc_final: 0.9051 (pttt) REVERT: IB 306 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8940 (tptp) REVERT: JB 1004 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: i 4 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8493 (tp30) REVERT: NB 102 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9139 (pttt) REVERT: NB 104 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8245 (pm20) REVERT: NB 106 LYS cc_start: 0.9234 (tttp) cc_final: 0.8717 (pptt) REVERT: OB 202 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9218 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: QB 1005 PHE cc_start: 0.9303 (t80) cc_final: 0.8675 (t80) outliers start: 220 outliers final: 153 residues processed: 523 average time/residue: 0.2143 time to fit residues: 138.0432 Evaluate side-chains 628 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 431 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1302 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 105 PHE Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.070682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.060175 restraints weight = 34584.718| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.20 r_work: 0.2649 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.351 12563 Z= 4.892 Angle : 4.052 30.003 16272 Z= 1.833 Chirality : 0.299 0.971 1152 Planarity : 0.017 0.061 2160 Dihedral : 20.580 82.805 1496 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 108.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.44 % Favored : 80.38 % Rotamer: Outliers : 26.85 % Allowed : 23.15 % Favored : 50.00 % Cbeta Deviations : 15.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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 aren not related in a simple way. whole: -5.93 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11016 (12528) covalent geometry : angle 4.05213 (16272) hydrogen bonds : bond 0.19119 ( 278) hydrogen bonds : angle 9.48484 ( 786) Misc. bond : bond 0.01075 ( 35) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 430 time to evaluate : 0.360 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: A 4 GLU cc_start: 0.8284 (mp0) cc_final: 0.7376 (mp0) REVERT: A 6 LYS cc_start: 0.9316 (mtmt) cc_final: 0.9046 (mtmt) REVERT: J 104 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8170 (mm-30) REVERT: M 1004 GLU cc_start: 0.8439 (mp0) cc_final: 0.7621 (mp0) REVERT: N 1104 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8501 (mm-30) REVERT: N 1106 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8634 (mmmm) REVERT: O 1206 LYS cc_start: 0.9271 (ttmm) cc_final: 0.9069 (ttmm) REVERT: P 1304 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8584 (mm-30) REVERT: B 4 GLU cc_start: 0.8398 (mp0) cc_final: 0.8068 (mp0) REVERT: Q 104 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8276 (mm-30) REVERT: Q 106 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8950 (mmmm) REVERT: S 307 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.9110 (m-80) REVERT: T 1004 GLU cc_start: 0.8695 (mp0) cc_final: 0.7953 (mp0) REVERT: T 1006 LYS cc_start: 0.9324 (mtmt) cc_final: 0.9020 (mtmt) REVERT: U 1104 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8192 (mm-30) REVERT: U 1106 LYS cc_start: 0.9031 (tptm) cc_final: 0.8658 (tptm) REVERT: W 1302 LYS cc_start: 0.9366 (mtpt) cc_final: 0.9009 (ttmm) REVERT: C 4 GLU cc_start: 0.8542 (mp0) cc_final: 0.7629 (mp0) REVERT: X 106 LYS cc_start: 0.9333 (mmmm) cc_final: 0.8989 (mmmm) REVERT: j 1004 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7874 (mp0) REVERT: j 1006 LYS cc_start: 0.9291 (mtmt) cc_final: 0.8875 (mtmt) REVERT: k 1104 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8236 (mm-30) REVERT: k 1106 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8817 (mmmm) REVERT: l 1202 LYS cc_start: 0.9386 (mtpt) cc_final: 0.9140 (mtpp) REVERT: D 4 GLU cc_start: 0.8393 (mp0) cc_final: 0.7672 (mp0) REVERT: D 6 LYS cc_start: 0.9289 (mtmt) cc_final: 0.8838 (mtmt) REVERT: D 7 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8713 (t80) REVERT: n 106 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8766 (mmmm) REVERT: o 202 LYS cc_start: 0.9456 (ttpt) cc_final: 0.9254 (ttpt) REVERT: r 1104 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: r 1106 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8807 (mmmm) REVERT: E 6 LYS cc_start: 0.9207 (mtmt) cc_final: 0.8941 (mtmt) REVERT: u 106 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8593 (mmmm) REVERT: v 206 LYS cc_start: 0.9443 (ttmm) cc_final: 0.9208 (ttmm) REVERT: w 302 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8989 (mmmm) REVERT: w 304 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8511 (mm-30) REVERT: w 307 PHE cc_start: 0.9562 (OUTLIER) cc_final: 0.8832 (m-80) REVERT: x 1006 LYS cc_start: 0.9155 (mtmt) cc_final: 0.8714 (mtmt) REVERT: y 1106 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8948 (mmmm) REVERT: F 6 LYS cc_start: 0.9247 (mtmt) cc_final: 0.8947 (mtmt) REVERT: 1 104 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8169 (mm-30) REVERT: 1 106 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8720 (mmmm) REVERT: 3 302 LYS cc_start: 0.9471 (ttpt) cc_final: 0.9102 (ttmm) REVERT: 5 1104 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8340 (mp0) REVERT: 5 1106 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8728 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9437 (mtpt) cc_final: 0.9069 (mtpp) REVERT: G 3 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: G 4 GLU cc_start: 0.8366 (mp0) cc_final: 0.7951 (mp0) REVERT: G 6 LYS cc_start: 0.9349 (mtmt) cc_final: 0.9024 (mtmt) REVERT: 8 104 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7935 (mm-30) REVERT: 8 106 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8678 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8592 (mp0) cc_final: 0.8251 (mp0) REVERT: CA 1104 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8216 (mm-30) REVERT: H 4 GLU cc_start: 0.4186 (OUTLIER) cc_final: 0.2844 (pm20) REVERT: FA 106 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8963 (mmmm) REVERT: HA 302 LYS cc_start: 0.9337 (mtpt) cc_final: 0.9038 (mmmm) REVERT: HA 304 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8599 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8496 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8800 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9249 (mtpt) cc_final: 0.9038 (pttm) REVERT: I 4 GLU cc_start: 0.8256 (mp0) cc_final: 0.7367 (mp0) REVERT: MA 106 LYS cc_start: 0.4929 (OUTLIER) cc_final: 0.3828 (tptt) REVERT: PA 1004 GLU cc_start: 0.8473 (mp0) cc_final: 0.7822 (mp0) REVERT: RA 1202 LYS cc_start: 0.9358 (mtpt) cc_final: 0.9124 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8567 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9270 (tttt) cc_final: 0.8871 (tttt) REVERT: SA 1307 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.8572 (m-80) REVERT: a 2 LYS cc_start: 0.9260 (tppt) cc_final: 0.9009 (tppt) REVERT: a 4 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8478 (tp30) REVERT: TA 106 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8865 (ptmm) REVERT: UA 202 LYS cc_start: 0.9441 (tttm) cc_final: 0.9032 (ttmm) REVERT: UA 204 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7882 (tm-30) REVERT: VA 302 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9090 (tptp) REVERT: WA 1002 LYS cc_start: 0.9282 (tppt) cc_final: 0.8901 (tppt) REVERT: WA 1004 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8627 (tp30) REVERT: YA 1204 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7861 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8816 (t80) REVERT: ZA 1304 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8604 (tm-30) REVERT: b 6 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9034 (ttpt) REVERT: aA 104 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8032 (tm-30) REVERT: bA 202 LYS cc_start: 0.9375 (tttm) cc_final: 0.9047 (ttmm) REVERT: bA 204 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8126 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8966 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9227 (tm-30) cc_final: 0.7819 (tm-30) REVERT: iA 204 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8173 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.9109 (t80) REVERT: nA 1306 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8938 (tptp) REVERT: d 4 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8089 (tp30) REVERT: oA 102 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9076 (tptm) REVERT: pA 204 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7664 (tm-30) REVERT: qA 306 LYS cc_start: 0.9127 (tptp) cc_final: 0.8857 (tptp) REVERT: tA 1204 GLU cc_start: 0.8719 (tm-30) cc_final: 0.7937 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8876 (tmtt) REVERT: e 4 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8412 (tp30) REVERT: e 6 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8828 (ttpt) REVERT: vA 104 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8569 (tm-30) REVERT: wA 202 LYS cc_start: 0.9344 (tttm) cc_final: 0.8976 (ttmm) REVERT: wA 204 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8276 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8362 (tp30) REVERT: 1A 1304 GLU cc_start: 0.9265 (tm-30) cc_final: 0.8598 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.9079 (t80) REVERT: f 2 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8901 (ttmt) REVERT: f 4 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8569 (tp30) REVERT: 3A 202 LYS cc_start: 0.9385 (tttm) cc_final: 0.9117 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8239 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8874 (tptp) REVERT: 4A 304 GLU cc_start: 0.9335 (tm-30) cc_final: 0.8434 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8055 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9016 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8348 (tm-30) REVERT: g 2 LYS cc_start: 0.9174 (tppt) cc_final: 0.8677 (tppt) REVERT: g 4 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8388 (tp30) REVERT: AB 202 LYS cc_start: 0.9450 (tttm) cc_final: 0.9109 (ttmm) REVERT: AB 204 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8058 (tm-30) REVERT: BB 302 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9053 (tptp) REVERT: BB 305 PHE cc_start: 0.9498 (OUTLIER) cc_final: 0.9262 (t80) REVERT: CB 1004 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8452 (tp30) REVERT: DB 1102 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9096 (tptm) REVERT: EB 1204 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7561 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8690 (tptp) REVERT: h 4 GLU cc_start: 0.8812 (tp30) cc_final: 0.8213 (pm20) REVERT: GB 103 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9141 (t80) REVERT: HB 202 LYS cc_start: 0.9432 (tttm) cc_final: 0.9046 (pttt) REVERT: IB 306 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8981 (tptp) REVERT: JB 1004 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8288 (tp30) REVERT: i 4 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8503 (tp30) REVERT: NB 102 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9141 (pttt) REVERT: NB 104 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8307 (pm20) REVERT: NB 106 LYS cc_start: 0.9222 (tttp) cc_final: 0.8700 (pptt) REVERT: OB 202 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9196 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: QB 1005 PHE cc_start: 0.9303 (t80) cc_final: 0.8718 (t80) outliers start: 232 outliers final: 166 residues processed: 529 average time/residue: 0.2233 time to fit residues: 145.3607 Evaluate side-chains 640 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 430 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1304 GLU Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain i residue 6 LYS Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain OB residue 202 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.070641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.060178 restraints weight = 34511.332| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.19 r_work: 0.2650 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.7602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.351 12563 Z= 4.896 Angle : 4.083 30.144 16272 Z= 1.847 Chirality : 0.300 0.969 1152 Planarity : 0.017 0.062 2160 Dihedral : 20.574 82.967 1496 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 108.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.97 % Favored : 79.86 % Rotamer: Outliers : 27.20 % Allowed : 23.26 % Favored : 49.54 % Cbeta Deviations : 15.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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 aren not related in a simple way. whole: -5.94 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11028 (12528) covalent geometry : angle 4.08346 (16272) hydrogen bonds : bond 0.19085 ( 278) hydrogen bonds : angle 9.48094 ( 786) Misc. bond : bond 0.01098 ( 35) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 428 time to evaluate : 0.452 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: A 4 GLU cc_start: 0.8248 (mp0) cc_final: 0.7277 (mp0) REVERT: A 6 LYS cc_start: 0.9312 (mtmt) cc_final: 0.8945 (mtmt) REVERT: J 104 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8136 (mm-30) REVERT: J 106 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8841 (tmmm) REVERT: M 1004 GLU cc_start: 0.8469 (mp0) cc_final: 0.7522 (mp0) REVERT: N 1104 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8490 (mm-30) REVERT: N 1106 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8656 (mmmm) REVERT: O 1206 LYS cc_start: 0.9272 (ttmm) cc_final: 0.9063 (ttmm) REVERT: P 1304 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8572 (mm-30) REVERT: B 4 GLU cc_start: 0.8390 (mp0) cc_final: 0.8043 (mp0) REVERT: Q 104 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8255 (mm-30) REVERT: Q 106 LYS cc_start: 0.9271 (mmmm) cc_final: 0.8955 (mmmm) REVERT: T 1004 GLU cc_start: 0.8693 (mp0) cc_final: 0.7967 (mp0) REVERT: T 1006 LYS cc_start: 0.9334 (mtmt) cc_final: 0.9022 (mtmt) REVERT: U 1104 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8183 (mm-30) REVERT: U 1106 LYS cc_start: 0.9037 (tptm) cc_final: 0.8674 (tptm) REVERT: C 4 GLU cc_start: 0.8570 (mp0) cc_final: 0.7631 (mp0) REVERT: X 106 LYS cc_start: 0.9348 (mmmm) cc_final: 0.9002 (mmmm) REVERT: j 1004 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: j 1006 LYS cc_start: 0.9295 (mtmt) cc_final: 0.8952 (mtmt) REVERT: k 1104 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8324 (mm-30) REVERT: k 1106 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8823 (mmmm) REVERT: l 1202 LYS cc_start: 0.9379 (mtpt) cc_final: 0.9123 (mtpp) REVERT: D 4 GLU cc_start: 0.8401 (mp0) cc_final: 0.7680 (mp0) REVERT: D 6 LYS cc_start: 0.9297 (mtmt) cc_final: 0.8845 (mtmt) REVERT: D 7 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8694 (t80) REVERT: n 106 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8786 (mmmm) REVERT: o 202 LYS cc_start: 0.9418 (ttpt) cc_final: 0.9137 (ttpt) REVERT: r 1104 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: r 1106 LYS cc_start: 0.9223 (mmmm) cc_final: 0.8827 (mmmm) REVERT: E 6 LYS cc_start: 0.9204 (mtmt) cc_final: 0.8943 (mtmt) REVERT: u 106 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8599 (mmmm) REVERT: v 206 LYS cc_start: 0.9445 (ttmm) cc_final: 0.9193 (ttmm) REVERT: w 302 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.8983 (mmmm) REVERT: w 307 PHE cc_start: 0.9548 (OUTLIER) cc_final: 0.8950 (m-80) REVERT: x 1006 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8752 (mtmt) REVERT: y 1106 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8956 (mmmm) REVERT: F 6 LYS cc_start: 0.9276 (mtmt) cc_final: 0.8981 (mtmt) REVERT: 1 104 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8184 (mm-30) REVERT: 1 106 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8724 (mmmm) REVERT: 3 302 LYS cc_start: 0.9467 (ttpt) cc_final: 0.9103 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8808 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9431 (mtpt) cc_final: 0.9059 (mtpp) REVERT: G 3 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7924 (m-80) REVERT: G 4 GLU cc_start: 0.8379 (mp0) cc_final: 0.7991 (mp0) REVERT: G 6 LYS cc_start: 0.9352 (mtmt) cc_final: 0.9029 (mtmt) REVERT: 8 104 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7950 (mm-30) REVERT: 8 106 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8665 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8473 (mp0) cc_final: 0.8112 (mp0) REVERT: CA 1104 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8224 (mm-30) REVERT: H 4 GLU cc_start: 0.4171 (OUTLIER) cc_final: 0.2830 (pm20) REVERT: FA 106 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8984 (mmmm) REVERT: HA 302 LYS cc_start: 0.9343 (mtpt) cc_final: 0.9035 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8265 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8773 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9254 (mtpt) cc_final: 0.9025 (pttp) REVERT: I 4 GLU cc_start: 0.8257 (mp0) cc_final: 0.7396 (mp0) REVERT: MA 106 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4518 (tptt) REVERT: PA 1004 GLU cc_start: 0.8474 (mp0) cc_final: 0.7810 (mp0) REVERT: PA 1006 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.9042 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9362 (mtpt) cc_final: 0.9124 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8567 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9280 (tttt) cc_final: 0.8867 (tttt) REVERT: SA 1307 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.8622 (m-80) REVERT: a 2 LYS cc_start: 0.9276 (tppt) cc_final: 0.9031 (tppt) REVERT: a 4 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8491 (tp30) REVERT: TA 104 GLU cc_start: 0.8930 (tm-30) cc_final: 0.7993 (tm-30) REVERT: TA 106 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8830 (ptmm) REVERT: UA 202 LYS cc_start: 0.9440 (tttm) cc_final: 0.9027 (ttmm) REVERT: UA 204 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7868 (tm-30) REVERT: VA 302 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9085 (tptp) REVERT: WA 1002 LYS cc_start: 0.9268 (tppt) cc_final: 0.8900 (tppt) REVERT: WA 1004 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8637 (tp30) REVERT: YA 1204 GLU cc_start: 0.8457 (tm-30) cc_final: 0.7878 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8825 (t80) REVERT: ZA 1304 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8592 (tm-30) REVERT: aA 104 GLU cc_start: 0.8881 (tm-30) cc_final: 0.7998 (tm-30) REVERT: bA 202 LYS cc_start: 0.9375 (tttm) cc_final: 0.9044 (ttmm) REVERT: bA 204 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8115 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8974 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9231 (tm-30) cc_final: 0.7834 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9305 (t80) cc_final: 0.8942 (t80) REVERT: c 4 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7856 (tm-30) REVERT: iA 204 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8206 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.9116 (t80) REVERT: nA 1306 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8935 (tptp) REVERT: d 2 LYS cc_start: 0.9204 (tppt) cc_final: 0.8894 (tppt) REVERT: d 4 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: oA 102 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9087 (tptm) REVERT: pA 204 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7650 (tm-30) REVERT: qA 306 LYS cc_start: 0.9132 (tptp) cc_final: 0.8863 (tptp) REVERT: rA 1006 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8973 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8717 (tm-30) cc_final: 0.7918 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8891 (tmtt) REVERT: e 4 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: e 6 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8837 (ttpt) REVERT: vA 104 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8571 (tm-30) REVERT: wA 202 LYS cc_start: 0.9345 (tttm) cc_final: 0.8975 (ttmm) REVERT: wA 204 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8294 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8333 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8337 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8610 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9084 (t80) REVERT: f 2 LYS cc_start: 0.9251 (ttmt) cc_final: 0.8900 (ttmt) REVERT: f 4 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8564 (tp30) REVERT: 3A 202 LYS cc_start: 0.9375 (tttm) cc_final: 0.8907 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8190 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8884 (tptp) REVERT: 4A 304 GLU cc_start: 0.9345 (tm-30) cc_final: 0.8445 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8066 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.9016 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8326 (tm-30) REVERT: g 2 LYS cc_start: 0.9165 (tppt) cc_final: 0.8675 (tppt) REVERT: g 4 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8391 (tp30) REVERT: AB 202 LYS cc_start: 0.9449 (tttm) cc_final: 0.9142 (ttmm) REVERT: AB 204 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8062 (tm-30) REVERT: BB 302 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9051 (tptp) REVERT: BB 305 PHE cc_start: 0.9500 (OUTLIER) cc_final: 0.9273 (t80) REVERT: CB 1004 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8459 (tp30) REVERT: DB 1102 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9100 (tptm) REVERT: EB 1204 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7578 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8731 (tptp) REVERT: h 4 GLU cc_start: 0.8812 (tp30) cc_final: 0.8218 (pm20) REVERT: GB 103 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.9140 (t80) REVERT: HB 202 LYS cc_start: 0.9420 (tttm) cc_final: 0.9045 (pttt) REVERT: IB 306 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8960 (tptp) REVERT: JB 1004 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8295 (tp30) REVERT: i 4 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8545 (tp30) REVERT: NB 102 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9143 (pttt) REVERT: NB 104 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8292 (pm20) REVERT: NB 106 LYS cc_start: 0.9228 (tttp) cc_final: 0.8716 (pptt) REVERT: QB 1004 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8093 (tp30) REVERT: QB 1005 PHE cc_start: 0.9318 (t80) cc_final: 0.8738 (t80) REVERT: QB 1006 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9069 (ttpt) outliers start: 235 outliers final: 167 residues processed: 531 average time/residue: 0.2192 time to fit residues: 143.3004 Evaluate side-chains 641 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 428 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1306 LYS Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1306 LYS Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.070301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.060004 restraints weight = 34475.096| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 3.15 r_work: 0.2654 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.7639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.346 12563 Z= 4.893 Angle : 4.091 30.639 16272 Z= 1.847 Chirality : 0.300 0.968 1152 Planarity : 0.017 0.064 2160 Dihedral : 20.530 83.281 1496 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 108.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.62 % Favored : 80.38 % Rotamer: Outliers : 27.55 % Allowed : 23.73 % Favored : 48.73 % Cbeta Deviations : 15.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.69 % 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 aren not related in a simple way. whole: -5.95 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.130 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11023 (12528) covalent geometry : angle 4.09129 (16272) hydrogen bonds : bond 0.19127 ( 278) hydrogen bonds : angle 9.50231 ( 786) Misc. bond : bond 0.01137 ( 35) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 431 time to evaluate : 0.488 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: A 4 GLU cc_start: 0.8249 (mp0) cc_final: 0.7276 (mp0) REVERT: A 6 LYS cc_start: 0.9305 (mtmt) cc_final: 0.8955 (mtmt) REVERT: J 104 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8195 (mm-30) REVERT: J 106 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8809 (tmmm) REVERT: M 1004 GLU cc_start: 0.8472 (mp0) cc_final: 0.7484 (mp0) REVERT: N 1104 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8489 (mm-30) REVERT: N 1106 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8623 (mmmm) REVERT: O 1206 LYS cc_start: 0.9270 (ttmm) cc_final: 0.9060 (ttmm) REVERT: P 1304 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8644 (mm-30) REVERT: B 4 GLU cc_start: 0.8404 (mp0) cc_final: 0.8066 (mp0) REVERT: B 5 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9194 (m-80) REVERT: Q 104 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8239 (mm-30) REVERT: Q 106 LYS cc_start: 0.9277 (mmmm) cc_final: 0.8966 (mmmm) REVERT: T 1004 GLU cc_start: 0.8685 (mp0) cc_final: 0.7952 (mp0) REVERT: T 1006 LYS cc_start: 0.9317 (mtmt) cc_final: 0.8961 (mtmt) REVERT: U 1104 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8183 (mm-30) REVERT: U 1106 LYS cc_start: 0.9040 (tptm) cc_final: 0.8668 (tptm) REVERT: W 1302 LYS cc_start: 0.9348 (mtpt) cc_final: 0.8961 (mtpp) REVERT: C 4 GLU cc_start: 0.8554 (mp0) cc_final: 0.7617 (mp0) REVERT: X 106 LYS cc_start: 0.9351 (mmmm) cc_final: 0.9008 (mmmm) REVERT: j 1004 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: j 1006 LYS cc_start: 0.9288 (mtmt) cc_final: 0.8882 (mtmt) REVERT: k 1104 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8305 (mm-30) REVERT: k 1106 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8825 (mmmm) REVERT: l 1202 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9115 (mtpp) REVERT: D 4 GLU cc_start: 0.8406 (mp0) cc_final: 0.7710 (mp0) REVERT: D 6 LYS cc_start: 0.9289 (mtmt) cc_final: 0.8837 (mtmt) REVERT: D 7 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8706 (t80) REVERT: n 106 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8759 (mmmm) REVERT: o 202 LYS cc_start: 0.9429 (ttpt) cc_final: 0.9138 (ttpt) REVERT: r 1104 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: r 1106 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8755 (mmmm) REVERT: E 6 LYS cc_start: 0.9196 (mtmt) cc_final: 0.8943 (mtmt) REVERT: u 106 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8583 (mmmm) REVERT: v 206 LYS cc_start: 0.9449 (ttmm) cc_final: 0.9186 (ttmm) REVERT: w 307 PHE cc_start: 0.9580 (OUTLIER) cc_final: 0.9008 (m-80) REVERT: x 1003 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8831 (m-80) REVERT: x 1006 LYS cc_start: 0.9140 (mtmt) cc_final: 0.8711 (mtmt) REVERT: y 1106 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8958 (mmmm) REVERT: F 6 LYS cc_start: 0.9277 (mtmt) cc_final: 0.8997 (mtmt) REVERT: 1 104 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8195 (mm-30) REVERT: 1 106 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8762 (mmmm) REVERT: 3 302 LYS cc_start: 0.9464 (ttpt) cc_final: 0.9098 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8797 (mmmm) REVERT: G 3 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: G 4 GLU cc_start: 0.8375 (mp0) cc_final: 0.8004 (mp0) REVERT: G 6 LYS cc_start: 0.9342 (mtmt) cc_final: 0.9019 (mtmt) REVERT: 8 104 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7936 (mm-30) REVERT: 8 106 LYS cc_start: 0.9077 (mmmm) cc_final: 0.8671 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8460 (mp0) cc_final: 0.8086 (mp0) REVERT: CA 1104 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8108 (mm-30) REVERT: H 4 GLU cc_start: 0.4195 (OUTLIER) cc_final: 0.2849 (pm20) REVERT: FA 106 LYS cc_start: 0.9225 (mmmm) cc_final: 0.8986 (mmmm) REVERT: HA 302 LYS cc_start: 0.9372 (mtpt) cc_final: 0.9041 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8234 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8787 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9247 (mtpt) cc_final: 0.9023 (pttp) REVERT: I 4 GLU cc_start: 0.8237 (mp0) cc_final: 0.7401 (mp0) REVERT: MA 106 LYS cc_start: 0.5134 (OUTLIER) cc_final: 0.3842 (tptt) REVERT: PA 1004 GLU cc_start: 0.8463 (mp0) cc_final: 0.7768 (mp0) REVERT: PA 1006 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9026 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9516 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: RA 1202 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9135 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8547 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9264 (tttt) cc_final: 0.8867 (tttt) REVERT: SA 1307 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: a 2 LYS cc_start: 0.9259 (tppt) cc_final: 0.9018 (tppt) REVERT: a 4 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8482 (tp30) REVERT: TA 106 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8898 (ptmm) REVERT: UA 202 LYS cc_start: 0.9433 (tttm) cc_final: 0.9019 (ttmm) REVERT: UA 204 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7848 (tm-30) REVERT: VA 302 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9083 (tptp) REVERT: WA 1002 LYS cc_start: 0.9263 (tppt) cc_final: 0.8875 (tppt) REVERT: WA 1004 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8633 (tp30) REVERT: YA 1204 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7878 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8817 (t80) REVERT: ZA 1304 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8605 (tm-30) REVERT: aA 104 GLU cc_start: 0.8881 (tm-30) cc_final: 0.7989 (tm-30) REVERT: bA 202 LYS cc_start: 0.9363 (tttm) cc_final: 0.9031 (ttmm) REVERT: bA 204 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8103 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9190 (ttmt) cc_final: 0.8950 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9227 (tm-30) cc_final: 0.7843 (tm-30) REVERT: c 4 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8419 (tp30) REVERT: iA 202 LYS cc_start: 0.9434 (tttm) cc_final: 0.9131 (mmmm) REVERT: iA 204 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8218 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.9111 (t80) REVERT: d 2 LYS cc_start: 0.9196 (tppt) cc_final: 0.8895 (tppt) REVERT: d 4 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8103 (tp30) REVERT: oA 102 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9082 (tptm) REVERT: pA 204 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7629 (tm-30) REVERT: qA 306 LYS cc_start: 0.9121 (tptp) cc_final: 0.8857 (tptp) REVERT: tA 1204 GLU cc_start: 0.8713 (tm-30) cc_final: 0.7895 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8915 (tmtt) REVERT: e 4 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: e 6 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8832 (ttpt) REVERT: vA 104 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8553 (tm-30) REVERT: wA 202 LYS cc_start: 0.9347 (tttm) cc_final: 0.8978 (ttmm) REVERT: wA 204 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8282 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8334 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8344 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8624 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9080 (t80) REVERT: f 2 LYS cc_start: 0.9234 (ttmt) cc_final: 0.8880 (ttmt) REVERT: f 4 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8555 (tp30) REVERT: 3A 202 LYS cc_start: 0.9362 (tttm) cc_final: 0.9103 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8165 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8880 (tptp) REVERT: 4A 304 GLU cc_start: 0.9341 (tm-30) cc_final: 0.8420 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8056 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8999 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8321 (tm-30) REVERT: g 2 LYS cc_start: 0.9155 (tppt) cc_final: 0.8664 (tppt) REVERT: g 4 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: AB 202 LYS cc_start: 0.9446 (tttm) cc_final: 0.9141 (ttmm) REVERT: AB 204 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8056 (tm-30) REVERT: BB 302 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9047 (tptp) REVERT: BB 305 PHE cc_start: 0.9502 (OUTLIER) cc_final: 0.9274 (t80) REVERT: CB 1004 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8462 (tp30) REVERT: DB 1102 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9089 (tptm) REVERT: EB 1204 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7576 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8735 (tptp) REVERT: h 4 GLU cc_start: 0.8788 (tp30) cc_final: 0.8175 (pm20) REVERT: GB 103 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.9139 (t80) REVERT: HB 202 LYS cc_start: 0.9409 (tttm) cc_final: 0.9044 (pttt) REVERT: IB 306 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8951 (tptp) REVERT: JB 1004 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8284 (tp30) REVERT: i 4 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8551 (tp30) REVERT: NB 102 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9145 (pttt) REVERT: NB 104 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8297 (pm20) REVERT: NB 106 LYS cc_start: 0.9221 (tttp) cc_final: 0.8725 (pptt) REVERT: QB 1004 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8050 (tp30) REVERT: QB 1005 PHE cc_start: 0.9314 (t80) cc_final: 0.8727 (t80) REVERT: QB 1006 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9029 (ttpt) outliers start: 238 outliers final: 177 residues processed: 534 average time/residue: 0.2225 time to fit residues: 146.3488 Evaluate side-chains 654 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 431 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1204 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain aA residue 106 LYS Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain tA residue 1206 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain PB residue 302 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain SB residue 1202 LYS Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.060074 restraints weight = 34182.088| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.13 r_work: 0.2653 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.7654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.345 12563 Z= 4.895 Angle : 4.077 30.460 16272 Z= 1.844 Chirality : 0.300 0.966 1152 Planarity : 0.017 0.064 2160 Dihedral : 20.492 83.483 1496 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 109.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.49 % Favored : 79.51 % Rotamer: Outliers : 27.20 % Allowed : 24.31 % Favored : 48.50 % Cbeta Deviations : 15.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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 aren not related in a simple way. whole: -5.96 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.54 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11027 (12528) covalent geometry : angle 4.07658 (16272) hydrogen bonds : bond 0.19126 ( 278) hydrogen bonds : angle 9.49337 ( 786) Misc. bond : bond 0.01099 ( 35) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 430 time to evaluate : 0.483 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: A 4 GLU cc_start: 0.8238 (mp0) cc_final: 0.7342 (mp0) REVERT: A 6 LYS cc_start: 0.9306 (mtmt) cc_final: 0.8942 (mtmt) REVERT: J 104 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8208 (mm-30) REVERT: J 106 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.8783 (tmmm) REVERT: M 1004 GLU cc_start: 0.8508 (mp0) cc_final: 0.7688 (mp0) REVERT: N 1104 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8527 (mm-30) REVERT: N 1106 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8653 (mmmm) REVERT: O 1206 LYS cc_start: 0.9266 (ttmm) cc_final: 0.9059 (ttmm) REVERT: B 4 GLU cc_start: 0.8382 (mp0) cc_final: 0.8052 (mp0) REVERT: Q 104 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8215 (mm-30) REVERT: Q 106 LYS cc_start: 0.9277 (mmmm) cc_final: 0.8966 (mmmm) REVERT: T 1004 GLU cc_start: 0.8686 (mp0) cc_final: 0.7950 (mp0) REVERT: T 1006 LYS cc_start: 0.9323 (mtmt) cc_final: 0.8950 (mtmt) REVERT: U 1104 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8187 (mm-30) REVERT: U 1106 LYS cc_start: 0.9053 (tptm) cc_final: 0.8684 (tptm) REVERT: W 1302 LYS cc_start: 0.9383 (mtpt) cc_final: 0.9031 (mtpp) REVERT: C 4 GLU cc_start: 0.8562 (mp0) cc_final: 0.7636 (mp0) REVERT: X 106 LYS cc_start: 0.9355 (mmmm) cc_final: 0.9013 (mmmm) REVERT: j 1004 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: j 1006 LYS cc_start: 0.9303 (mtmt) cc_final: 0.8944 (mtmt) REVERT: k 1104 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8332 (mm-30) REVERT: k 1106 LYS cc_start: 0.9136 (mmmm) cc_final: 0.8836 (mmmm) REVERT: l 1202 LYS cc_start: 0.9367 (mtpt) cc_final: 0.9002 (mtpp) REVERT: D 4 GLU cc_start: 0.8402 (mp0) cc_final: 0.7729 (mp0) REVERT: D 6 LYS cc_start: 0.9295 (mtmt) cc_final: 0.8852 (mtmt) REVERT: D 7 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.8706 (t80) REVERT: n 106 LYS cc_start: 0.9192 (mmmm) cc_final: 0.8763 (mmmm) REVERT: o 202 LYS cc_start: 0.9426 (ttpt) cc_final: 0.9142 (ttpt) REVERT: r 1104 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: r 1106 LYS cc_start: 0.9185 (mmmm) cc_final: 0.8746 (mmmm) REVERT: E 6 LYS cc_start: 0.9203 (mtmt) cc_final: 0.8957 (mtmt) REVERT: u 106 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8601 (mmmm) REVERT: v 206 LYS cc_start: 0.9446 (ttmm) cc_final: 0.9193 (ttmm) REVERT: w 302 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8968 (mmmm) REVERT: w 307 PHE cc_start: 0.9535 (OUTLIER) cc_final: 0.9086 (m-80) REVERT: x 1003 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8858 (m-80) REVERT: x 1006 LYS cc_start: 0.9143 (mtmt) cc_final: 0.8788 (mtmt) REVERT: y 1106 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8952 (mmmm) REVERT: F 6 LYS cc_start: 0.9283 (mtmt) cc_final: 0.9016 (mtmt) REVERT: 1 104 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8203 (mm-30) REVERT: 1 106 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8781 (mmmm) REVERT: 3 302 LYS cc_start: 0.9464 (ttpt) cc_final: 0.9100 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8817 (mmmm) REVERT: G 3 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: G 4 GLU cc_start: 0.8383 (mp0) cc_final: 0.8007 (mp0) REVERT: G 6 LYS cc_start: 0.9354 (mtmt) cc_final: 0.9042 (mtmt) REVERT: 8 104 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7954 (mm-30) REVERT: 8 106 LYS cc_start: 0.9078 (mmmm) cc_final: 0.8674 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8443 (mp0) cc_final: 0.8058 (mp0) REVERT: CA 1104 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8109 (mm-30) REVERT: H 4 GLU cc_start: 0.4168 (OUTLIER) cc_final: 0.2843 (pm20) REVERT: FA 106 LYS cc_start: 0.9245 (mmmm) cc_final: 0.9003 (mmmm) REVERT: HA 302 LYS cc_start: 0.9354 (mtpt) cc_final: 0.9056 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8238 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8794 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9257 (mtpt) cc_final: 0.9025 (pttp) REVERT: I 4 GLU cc_start: 0.8239 (mp0) cc_final: 0.7414 (mp0) REVERT: MA 106 LYS cc_start: 0.5144 (OUTLIER) cc_final: 0.4125 (tptt) REVERT: PA 1004 GLU cc_start: 0.8464 (mp0) cc_final: 0.7773 (mp0) REVERT: PA 1006 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.9033 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9519 (OUTLIER) cc_final: 0.8926 (m-80) REVERT: RA 1202 LYS cc_start: 0.9371 (mtpt) cc_final: 0.9134 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8560 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9265 (tttt) cc_final: 0.8867 (tttt) REVERT: SA 1307 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.8634 (m-80) REVERT: a 2 LYS cc_start: 0.9266 (tppt) cc_final: 0.9040 (tppt) REVERT: a 4 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8500 (tp30) REVERT: TA 106 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8896 (ptmm) REVERT: UA 202 LYS cc_start: 0.9441 (tttm) cc_final: 0.9035 (ttmm) REVERT: UA 204 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7846 (tm-30) REVERT: VA 302 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9084 (tptp) REVERT: WA 1002 LYS cc_start: 0.9267 (tppt) cc_final: 0.8878 (tppt) REVERT: WA 1004 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8640 (tp30) REVERT: YA 1204 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7860 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.8823 (t80) REVERT: ZA 1304 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8603 (tm-30) REVERT: aA 104 GLU cc_start: 0.8848 (tm-30) cc_final: 0.7988 (tm-30) REVERT: bA 202 LYS cc_start: 0.9380 (tttm) cc_final: 0.9049 (ttmm) REVERT: bA 204 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8065 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9209 (ttmt) cc_final: 0.8975 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9227 (tm-30) cc_final: 0.7838 (tm-30) REVERT: iA 202 LYS cc_start: 0.9430 (tttm) cc_final: 0.9130 (mmmm) REVERT: iA 204 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8231 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.9114 (t80) REVERT: d 2 LYS cc_start: 0.9202 (tppt) cc_final: 0.8901 (tppt) REVERT: d 4 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: oA 102 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9104 (tptm) REVERT: pA 204 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7636 (tm-30) REVERT: qA 306 LYS cc_start: 0.9131 (tptp) cc_final: 0.8862 (tptp) REVERT: tA 1204 GLU cc_start: 0.8720 (tm-30) cc_final: 0.7897 (tm-30) REVERT: uA 1307 PHE cc_start: 0.9461 (OUTLIER) cc_final: 0.9158 (t80) REVERT: e 4 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8386 (tp30) REVERT: e 6 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8841 (ttpt) REVERT: vA 104 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8566 (tm-30) REVERT: wA 202 LYS cc_start: 0.9344 (tttm) cc_final: 0.8972 (ttmm) REVERT: wA 204 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8294 (tm-30) REVERT: wA 206 LYS cc_start: 0.9237 (tmtt) cc_final: 0.8856 (tmtt) REVERT: yA 1004 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8338 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8634 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9085 (t80) REVERT: f 2 LYS cc_start: 0.9243 (ttmt) cc_final: 0.8893 (ttmt) REVERT: f 4 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8562 (tp30) REVERT: 3A 202 LYS cc_start: 0.9362 (tttm) cc_final: 0.9064 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8166 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8827 (tptp) REVERT: 4A 304 GLU cc_start: 0.9346 (tm-30) cc_final: 0.8437 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8059 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8978 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8321 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.8882 (tptp) cc_final: 0.8631 (tptp) REVERT: g 2 LYS cc_start: 0.9176 (tppt) cc_final: 0.8695 (tppt) REVERT: g 4 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8389 (tp30) REVERT: AB 202 LYS cc_start: 0.9439 (tttm) cc_final: 0.9148 (ttmm) REVERT: AB 204 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8072 (tm-30) REVERT: BB 302 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9043 (tptp) REVERT: BB 305 PHE cc_start: 0.9502 (OUTLIER) cc_final: 0.9276 (t80) REVERT: CB 1004 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8472 (tp30) REVERT: DB 1102 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9092 (tptm) REVERT: EB 1204 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7573 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8734 (tptp) REVERT: h 4 GLU cc_start: 0.8779 (tp30) cc_final: 0.8173 (pm20) REVERT: GB 103 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9140 (t80) REVERT: HB 202 LYS cc_start: 0.9413 (tttm) cc_final: 0.9044 (pttt) REVERT: IB 306 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8943 (tptp) REVERT: JB 1004 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8298 (tp30) REVERT: i 4 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8564 (tp30) REVERT: NB 102 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9146 (pttt) REVERT: NB 104 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8293 (pm20) REVERT: NB 106 LYS cc_start: 0.9220 (tttp) cc_final: 0.8724 (pptt) REVERT: QB 1004 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: QB 1005 PHE cc_start: 0.9310 (t80) cc_final: 0.8725 (t80) REVERT: QB 1006 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9038 (ttpt) outliers start: 235 outliers final: 175 residues processed: 537 average time/residue: 0.2169 time to fit residues: 143.5542 Evaluate side-chains 650 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 430 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1204 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.070388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060059 restraints weight = 34368.990| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.15 r_work: 0.2653 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.339 12563 Z= 4.893 Angle : 4.072 30.606 16272 Z= 1.840 Chirality : 0.300 0.968 1152 Planarity : 0.017 0.065 2160 Dihedral : 20.521 83.339 1496 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 109.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.49 % Favored : 79.51 % Rotamer: Outliers : 27.31 % Allowed : 24.19 % Favored : 48.50 % Cbeta Deviations : 15.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % 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 aren not related in a simple way. whole: -5.96 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.53 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.131 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11023 (12528) covalent geometry : angle 4.07183 (16272) hydrogen bonds : bond 0.19224 ( 278) hydrogen bonds : angle 9.49953 ( 786) Misc. bond : bond 0.01108 ( 35) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 429 time to evaluate : 0.463 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: A 4 GLU cc_start: 0.8247 (mp0) cc_final: 0.7346 (mp0) REVERT: A 6 LYS cc_start: 0.9304 (mtmt) cc_final: 0.8958 (mtmt) REVERT: J 104 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8196 (mm-30) REVERT: J 106 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8778 (tmmm) REVERT: M 1004 GLU cc_start: 0.8324 (mp0) cc_final: 0.7552 (mp0) REVERT: N 1104 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8496 (mm-30) REVERT: N 1106 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8652 (mmmm) REVERT: O 1206 LYS cc_start: 0.9263 (ttmm) cc_final: 0.9055 (ttmm) REVERT: B 4 GLU cc_start: 0.8397 (mp0) cc_final: 0.8121 (mp0) REVERT: Q 104 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8197 (mm-30) REVERT: Q 106 LYS cc_start: 0.9284 (mmmm) cc_final: 0.8974 (mmmm) REVERT: T 1004 GLU cc_start: 0.8692 (mp0) cc_final: 0.7957 (mp0) REVERT: T 1006 LYS cc_start: 0.9319 (mtmt) cc_final: 0.8896 (mtmt) REVERT: U 1104 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8188 (mm-30) REVERT: U 1106 LYS cc_start: 0.9053 (tptm) cc_final: 0.8683 (tptm) REVERT: W 1302 LYS cc_start: 0.9394 (mtpt) cc_final: 0.9048 (mtpp) REVERT: C 4 GLU cc_start: 0.8564 (mp0) cc_final: 0.7629 (mp0) REVERT: X 106 LYS cc_start: 0.9363 (mmmm) cc_final: 0.9017 (mmmm) REVERT: j 1004 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: j 1006 LYS cc_start: 0.9303 (mtmt) cc_final: 0.8939 (mtmt) REVERT: k 1104 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8336 (mm-30) REVERT: k 1106 LYS cc_start: 0.9140 (mmmm) cc_final: 0.8841 (mmmm) REVERT: l 1202 LYS cc_start: 0.9366 (mtpt) cc_final: 0.9004 (mtpp) REVERT: D 4 GLU cc_start: 0.8397 (mp0) cc_final: 0.7726 (mp0) REVERT: D 6 LYS cc_start: 0.9290 (mtmt) cc_final: 0.8860 (mtmt) REVERT: D 7 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8708 (t80) REVERT: n 106 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8725 (mmmm) REVERT: o 202 LYS cc_start: 0.9432 (ttpt) cc_final: 0.9158 (ttpt) REVERT: r 1104 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7980 (mm-30) REVERT: r 1106 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8738 (mmmm) REVERT: E 6 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8966 (mtmt) REVERT: u 106 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8607 (mmmm) REVERT: v 206 LYS cc_start: 0.9455 (ttmm) cc_final: 0.9195 (ttmm) REVERT: w 302 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8954 (mmmm) REVERT: w 307 PHE cc_start: 0.9576 (OUTLIER) cc_final: 0.9000 (m-80) REVERT: x 1003 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8885 (m-80) REVERT: x 1006 LYS cc_start: 0.9136 (mtmt) cc_final: 0.8770 (mtmt) REVERT: y 1106 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8952 (mmmm) REVERT: F 6 LYS cc_start: 0.9255 (mtmt) cc_final: 0.8986 (mtmt) REVERT: 1 104 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8218 (mm-30) REVERT: 1 106 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8803 (mmmm) REVERT: 3 302 LYS cc_start: 0.9467 (ttpt) cc_final: 0.9105 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8810 (mmmm) REVERT: G 3 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: G 4 GLU cc_start: 0.8383 (mp0) cc_final: 0.8007 (mp0) REVERT: G 6 LYS cc_start: 0.9357 (mtmt) cc_final: 0.9050 (mtmt) REVERT: 8 104 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7959 (mm-30) REVERT: 8 106 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8671 (mmmm) REVERT: CA 1104 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8115 (mm-30) REVERT: H 4 GLU cc_start: 0.4178 (OUTLIER) cc_final: 0.2841 (pm20) REVERT: FA 106 LYS cc_start: 0.9247 (mmmm) cc_final: 0.9004 (mmmm) REVERT: HA 302 LYS cc_start: 0.9367 (mtpt) cc_final: 0.9053 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8270 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8794 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9249 (mtpt) cc_final: 0.9020 (pttp) REVERT: I 4 GLU cc_start: 0.8246 (mp0) cc_final: 0.7427 (mp0) REVERT: MA 106 LYS cc_start: 0.5075 (OUTLIER) cc_final: 0.3892 (tptt) REVERT: PA 1004 GLU cc_start: 0.8439 (mp0) cc_final: 0.7773 (mp0) REVERT: PA 1006 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9053 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9539 (OUTLIER) cc_final: 0.8961 (m-80) REVERT: RA 1202 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9129 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8557 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9262 (tttt) cc_final: 0.8864 (tttt) REVERT: SA 1307 PHE cc_start: 0.9492 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: a 2 LYS cc_start: 0.9258 (tppt) cc_final: 0.9037 (tppt) REVERT: a 4 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8494 (tp30) REVERT: TA 106 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8915 (ptmm) REVERT: UA 202 LYS cc_start: 0.9440 (tttm) cc_final: 0.9035 (ttmm) REVERT: UA 204 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7846 (tm-30) REVERT: VA 302 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9086 (tptp) REVERT: WA 1002 LYS cc_start: 0.9272 (tppt) cc_final: 0.8881 (tppt) REVERT: WA 1004 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8633 (tp30) REVERT: YA 1204 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7847 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8820 (t80) REVERT: ZA 1304 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8605 (tm-30) REVERT: aA 104 GLU cc_start: 0.8847 (tm-30) cc_final: 0.7980 (tm-30) REVERT: bA 202 LYS cc_start: 0.9386 (tttm) cc_final: 0.9057 (ttmm) REVERT: bA 204 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8065 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8966 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9219 (tm-30) cc_final: 0.7829 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9255 (t80) cc_final: 0.8873 (t80) REVERT: iA 202 LYS cc_start: 0.9435 (tttm) cc_final: 0.9128 (mmmm) REVERT: iA 204 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8213 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.9112 (t80) REVERT: d 2 LYS cc_start: 0.9207 (tppt) cc_final: 0.8899 (tppt) REVERT: d 4 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: oA 102 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9110 (tptm) REVERT: pA 204 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7638 (tm-30) REVERT: qA 306 LYS cc_start: 0.9139 (tptp) cc_final: 0.8872 (tptp) REVERT: tA 1204 GLU cc_start: 0.8733 (tm-30) cc_final: 0.7905 (tm-30) REVERT: uA 1307 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.9181 (t80) REVERT: e 4 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8409 (tp30) REVERT: e 6 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8844 (ttpt) REVERT: vA 104 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8560 (tm-30) REVERT: wA 202 LYS cc_start: 0.9345 (tttm) cc_final: 0.8975 (ttmm) REVERT: wA 204 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8290 (tm-30) REVERT: wA 206 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8852 (tmtt) REVERT: yA 1004 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8335 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8633 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9083 (t80) REVERT: f 2 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8896 (ttmt) REVERT: f 4 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8569 (tp30) REVERT: 3A 202 LYS cc_start: 0.9370 (tttm) cc_final: 0.9070 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8146 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8850 (tptp) REVERT: 4A 304 GLU cc_start: 0.9347 (tm-30) cc_final: 0.8437 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8018 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8922 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8321 (tm-30) REVERT: 8A 1306 LYS cc_start: 0.8877 (tptp) cc_final: 0.8626 (tptp) REVERT: g 2 LYS cc_start: 0.9179 (tppt) cc_final: 0.8697 (tppt) REVERT: g 4 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8389 (tp30) REVERT: AB 202 LYS cc_start: 0.9444 (tttm) cc_final: 0.9154 (ttmm) REVERT: AB 204 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8066 (tm-30) REVERT: BB 302 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9042 (tptp) REVERT: BB 305 PHE cc_start: 0.9486 (OUTLIER) cc_final: 0.9262 (t80) REVERT: CB 1004 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: DB 1102 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9101 (tptm) REVERT: EB 1204 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7564 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8727 (tptp) REVERT: h 4 GLU cc_start: 0.8774 (tp30) cc_final: 0.8172 (pm20) REVERT: GB 103 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9136 (t80) REVERT: HB 202 LYS cc_start: 0.9410 (tttm) cc_final: 0.9040 (pttt) REVERT: IB 306 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8900 (tptp) REVERT: JB 1004 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8293 (tp30) REVERT: i 4 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: NB 102 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9146 (pttt) REVERT: NB 104 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8292 (pm20) REVERT: NB 106 LYS cc_start: 0.9228 (tttp) cc_final: 0.8731 (pptt) REVERT: QB 1004 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: QB 1005 PHE cc_start: 0.9303 (t80) cc_final: 0.8710 (t80) REVERT: QB 1006 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9027 (ttpt) outliers start: 236 outliers final: 179 residues processed: 534 average time/residue: 0.2205 time to fit residues: 144.8662 Evaluate side-chains 654 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 429 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain K residue 202 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain R residue 203 PHE Chi-restraints excluded: chain R residue 206 LYS Chi-restraints excluded: chain R residue 207 PHE Chi-restraints excluded: chain S residue 302 LYS Chi-restraints excluded: chain S residue 307 PHE Chi-restraints excluded: chain V residue 1206 LYS Chi-restraints excluded: chain W residue 1307 PHE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 7 PHE Chi-restraints excluded: chain Y residue 206 LYS Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain j residue 1004 GLU Chi-restraints excluded: chain l residue 1204 GLU Chi-restraints excluded: chain l residue 1206 LYS Chi-restraints excluded: chain l residue 1207 PHE Chi-restraints excluded: chain m residue 1304 GLU Chi-restraints excluded: chain m residue 1306 LYS Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain r residue 1104 GLU Chi-restraints excluded: chain t residue 1307 PHE Chi-restraints excluded: chain w residue 302 LYS Chi-restraints excluded: chain w residue 307 PHE Chi-restraints excluded: chain x residue 1002 LYS Chi-restraints excluded: chain x residue 1003 PHE Chi-restraints excluded: chain y residue 1106 LYS Chi-restraints excluded: chain z residue 1204 GLU Chi-restraints excluded: chain 0 residue 1307 PHE Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain 1 residue 106 LYS Chi-restraints excluded: chain 2 residue 206 LYS Chi-restraints excluded: chain 3 residue 307 PHE Chi-restraints excluded: chain 5 residue 1106 LYS Chi-restraints excluded: chain 5 residue 1107 PHE Chi-restraints excluded: chain 6 residue 1206 LYS Chi-restraints excluded: chain G residue 3 PHE Chi-restraints excluded: chain 9 residue 202 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain CA residue 1106 LYS Chi-restraints excluded: chain DA residue 1206 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain GA residue 202 LYS Chi-restraints excluded: chain GA residue 204 GLU Chi-restraints excluded: chain GA residue 206 LYS Chi-restraints excluded: chain GA residue 207 PHE Chi-restraints excluded: chain HA residue 306 LYS Chi-restraints excluded: chain IA residue 1006 LYS Chi-restraints excluded: chain KA residue 1204 GLU Chi-restraints excluded: chain KA residue 1207 PHE Chi-restraints excluded: chain LA residue 1307 PHE Chi-restraints excluded: chain I residue 6 LYS Chi-restraints excluded: chain MA residue 106 LYS Chi-restraints excluded: chain MA residue 107 PHE Chi-restraints excluded: chain NA residue 206 LYS Chi-restraints excluded: chain OA residue 302 LYS Chi-restraints excluded: chain OA residue 304 GLU Chi-restraints excluded: chain OA residue 307 PHE Chi-restraints excluded: chain PA residue 1006 LYS Chi-restraints excluded: chain PA residue 1007 PHE Chi-restraints excluded: chain QA residue 1106 LYS Chi-restraints excluded: chain RA residue 1207 PHE Chi-restraints excluded: chain SA residue 1302 LYS Chi-restraints excluded: chain SA residue 1307 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain TA residue 102 LYS Chi-restraints excluded: chain TA residue 106 LYS Chi-restraints excluded: chain VA residue 302 LYS Chi-restraints excluded: chain VA residue 303 PHE Chi-restraints excluded: chain VA residue 305 PHE Chi-restraints excluded: chain VA residue 307 PHE Chi-restraints excluded: chain WA residue 1004 GLU Chi-restraints excluded: chain XA residue 1102 LYS Chi-restraints excluded: chain XA residue 1103 PHE Chi-restraints excluded: chain XA residue 1105 PHE Chi-restraints excluded: chain XA residue 1106 LYS Chi-restraints excluded: chain YA residue 1206 LYS Chi-restraints excluded: chain ZA residue 1302 LYS Chi-restraints excluded: chain ZA residue 1303 PHE Chi-restraints excluded: chain ZA residue 1307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain aA residue 102 LYS Chi-restraints excluded: chain aA residue 105 PHE Chi-restraints excluded: chain cA residue 305 PHE Chi-restraints excluded: chain cA residue 307 PHE Chi-restraints excluded: chain dA residue 1004 GLU Chi-restraints excluded: chain dA residue 1006 LYS Chi-restraints excluded: chain eA residue 1102 LYS Chi-restraints excluded: chain eA residue 1103 PHE Chi-restraints excluded: chain eA residue 1105 PHE Chi-restraints excluded: chain fA residue 1202 LYS Chi-restraints excluded: chain fA residue 1204 GLU Chi-restraints excluded: chain gA residue 1302 LYS Chi-restraints excluded: chain gA residue 1303 PHE Chi-restraints excluded: chain gA residue 1307 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain hA residue 103 PHE Chi-restraints excluded: chain hA residue 105 PHE Chi-restraints excluded: chain jA residue 302 LYS Chi-restraints excluded: chain jA residue 303 PHE Chi-restraints excluded: chain jA residue 305 PHE Chi-restraints excluded: chain jA residue 307 PHE Chi-restraints excluded: chain kA residue 1002 LYS Chi-restraints excluded: chain lA residue 1102 LYS Chi-restraints excluded: chain lA residue 1103 PHE Chi-restraints excluded: chain lA residue 1105 PHE Chi-restraints excluded: chain lA residue 1106 LYS Chi-restraints excluded: chain mA residue 1206 LYS Chi-restraints excluded: chain nA residue 1302 LYS Chi-restraints excluded: chain nA residue 1303 PHE Chi-restraints excluded: chain nA residue 1305 PHE Chi-restraints excluded: chain nA residue 1307 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain oA residue 102 LYS Chi-restraints excluded: chain oA residue 103 PHE Chi-restraints excluded: chain oA residue 105 PHE Chi-restraints excluded: chain oA residue 106 LYS Chi-restraints excluded: chain pA residue 203 PHE Chi-restraints excluded: chain qA residue 303 PHE Chi-restraints excluded: chain qA residue 305 PHE Chi-restraints excluded: chain qA residue 307 PHE Chi-restraints excluded: chain rA residue 1006 LYS Chi-restraints excluded: chain sA residue 1102 LYS Chi-restraints excluded: chain sA residue 1103 PHE Chi-restraints excluded: chain sA residue 1105 PHE Chi-restraints excluded: chain tA residue 1202 LYS Chi-restraints excluded: chain uA residue 1303 PHE Chi-restraints excluded: chain uA residue 1305 PHE Chi-restraints excluded: chain uA residue 1307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain vA residue 102 LYS Chi-restraints excluded: chain vA residue 103 PHE Chi-restraints excluded: chain vA residue 105 PHE Chi-restraints excluded: chain wA residue 206 LYS Chi-restraints excluded: chain xA residue 303 PHE Chi-restraints excluded: chain xA residue 305 PHE Chi-restraints excluded: chain xA residue 307 PHE Chi-restraints excluded: chain yA residue 1004 GLU Chi-restraints excluded: chain zA residue 1103 PHE Chi-restraints excluded: chain zA residue 1105 PHE Chi-restraints excluded: chain zA residue 1106 LYS Chi-restraints excluded: chain 0A residue 1202 LYS Chi-restraints excluded: chain 1A residue 1302 LYS Chi-restraints excluded: chain 1A residue 1303 PHE Chi-restraints excluded: chain 1A residue 1305 PHE Chi-restraints excluded: chain 1A residue 1306 LYS Chi-restraints excluded: chain 1A residue 1307 PHE Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 2A residue 106 LYS Chi-restraints excluded: chain 4A residue 302 LYS Chi-restraints excluded: chain 4A residue 303 PHE Chi-restraints excluded: chain 4A residue 305 PHE Chi-restraints excluded: chain 4A residue 306 LYS Chi-restraints excluded: chain 4A residue 307 PHE Chi-restraints excluded: chain 5A residue 1002 LYS Chi-restraints excluded: chain 5A residue 1004 GLU Chi-restraints excluded: chain 6A residue 1102 LYS Chi-restraints excluded: chain 6A residue 1103 PHE Chi-restraints excluded: chain 6A residue 1105 PHE Chi-restraints excluded: chain 6A residue 1106 LYS Chi-restraints excluded: chain 7A residue 1202 LYS Chi-restraints excluded: chain 8A residue 1302 LYS Chi-restraints excluded: chain 8A residue 1303 PHE Chi-restraints excluded: chain 8A residue 1305 PHE Chi-restraints excluded: chain 8A residue 1307 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain 9A residue 102 LYS Chi-restraints excluded: chain 9A residue 103 PHE Chi-restraints excluded: chain 9A residue 106 LYS Chi-restraints excluded: chain AB residue 206 LYS Chi-restraints excluded: chain BB residue 302 LYS Chi-restraints excluded: chain BB residue 303 PHE Chi-restraints excluded: chain BB residue 305 PHE Chi-restraints excluded: chain BB residue 307 PHE Chi-restraints excluded: chain CB residue 1004 GLU Chi-restraints excluded: chain DB residue 1102 LYS Chi-restraints excluded: chain DB residue 1103 PHE Chi-restraints excluded: chain DB residue 1105 PHE Chi-restraints excluded: chain EB residue 1202 LYS Chi-restraints excluded: chain EB residue 1206 LYS Chi-restraints excluded: chain FB residue 1302 LYS Chi-restraints excluded: chain FB residue 1303 PHE Chi-restraints excluded: chain FB residue 1307 PHE Chi-restraints excluded: chain h residue 3 PHE Chi-restraints excluded: chain GB residue 102 LYS Chi-restraints excluded: chain GB residue 103 PHE Chi-restraints excluded: chain GB residue 105 PHE Chi-restraints excluded: chain GB residue 106 LYS Chi-restraints excluded: chain HB residue 204 GLU Chi-restraints excluded: chain HB residue 206 LYS Chi-restraints excluded: chain IB residue 305 PHE Chi-restraints excluded: chain IB residue 306 LYS Chi-restraints excluded: chain IB residue 307 PHE Chi-restraints excluded: chain JB residue 1002 LYS Chi-restraints excluded: chain JB residue 1004 GLU Chi-restraints excluded: chain KB residue 1102 LYS Chi-restraints excluded: chain KB residue 1103 PHE Chi-restraints excluded: chain KB residue 1105 PHE Chi-restraints excluded: chain KB residue 1106 LYS Chi-restraints excluded: chain LB residue 1202 LYS Chi-restraints excluded: chain LB residue 1204 GLU Chi-restraints excluded: chain LB residue 1206 LYS Chi-restraints excluded: chain MB residue 1303 PHE Chi-restraints excluded: chain MB residue 1307 PHE Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain NB residue 102 LYS Chi-restraints excluded: chain PB residue 303 PHE Chi-restraints excluded: chain PB residue 305 PHE Chi-restraints excluded: chain PB residue 307 PHE Chi-restraints excluded: chain QB residue 1002 LYS Chi-restraints excluded: chain QB residue 1004 GLU Chi-restraints excluded: chain QB residue 1006 LYS Chi-restraints excluded: chain RB residue 1105 PHE Chi-restraints excluded: chain TB residue 1303 PHE Chi-restraints excluded: chain TB residue 1305 PHE Chi-restraints excluded: chain TB residue 1307 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060097 restraints weight = 34385.388| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.18 r_work: 0.2651 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.7678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.339 12563 Z= 4.894 Angle : 4.072 30.617 16272 Z= 1.839 Chirality : 0.300 0.969 1152 Planarity : 0.018 0.085 2160 Dihedral : 20.515 83.376 1496 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 109.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.31 % Favored : 79.69 % Rotamer: Outliers : 27.08 % Allowed : 24.54 % Favored : 48.38 % Cbeta Deviations : 15.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % 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 aren not related in a simple way. whole: -5.96 (0.23), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.54 (0.18), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.129 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11027 (12528) covalent geometry : angle 4.07162 (16272) hydrogen bonds : bond 0.19235 ( 278) hydrogen bonds : angle 9.49891 ( 786) Misc. bond : bond 0.01089 ( 35) =============================================================================== Job complete usr+sys time: 3072.23 seconds wall clock time: 53 minutes 43.52 seconds (3223.52 seconds total)