Starting phenix.real_space_refine on Wed Mar 4 08:12:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqh_23486/03_2026/7lqh_23486.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqh_23486/03_2026/7lqh_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_23486/03_2026/7lqh_23486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqh_23486/03_2026/7lqh_23486.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqh_23486/03_2026/7lqh_23486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqh_23486/03_2026/7lqh_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-dev-5986/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: 2.66, per 1000 atoms: 0.22 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: 0.95 Conformation dependent library (CDL) restraints added in 337.6 milliseconds 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: 0.30 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: 1.69 Time building geometry restraints manager: 1.28 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- 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 are 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 : 0.399 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: 0.7492 (mp0) cc_final: 0.6748 (pm20) REVERT: S 306 LYS cc_start: 0.8628 (tttt) cc_final: 0.8357 (mttt) REVERT: Y 206 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8179 (ttmm) REVERT: Z 306 LYS cc_start: 0.8563 (tttt) cc_final: 0.8261 (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: 0.8340 (mttt) REVERT: o 204 GLU cc_start: 0.7422 (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: 0.7749 (mm-30) cc_final: 0.7091 (mm-30) REVERT: w 306 LYS cc_start: 0.8690 (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: 0.7621 (mm-30) cc_final: 0.7144 (mm-30) REVERT: 0 1306 LYS cc_start: 0.8595 (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: 0.7149 (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: 0.6533 (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: 0.7038 (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: 0.8343 (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: 0.8547 (t80) cc_final: 0.8265 (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: 0.8996 (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: 0.8426 (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: 0.8657 (tttm) cc_final: 0.8373 (tttm) REVERT: c 5 PHE cc_start: 0.8933 (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: 0.8869 (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: 0.8704 (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: 0.8846 (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: 0.8827 (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: 0.8738 (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: 0.9168 (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: 0.9153 (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: 0.9122 (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: 0.8928 (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: 0.9079 (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: 0.1933 time to fit residues: 117.4345 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 : 0.353 ------------------------------------------------------------------------------- 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 are 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 : 0.437 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: 0.7534 (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: 0.8319 (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: 0.8612 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: j 1006 LYS cc_start: 0.9247 (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: 0.9278 (ttmm) cc_final: 0.9058 (ttmm) REVERT: D 4 GLU cc_start: 0.8361 (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: 0.7972 (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: 0.8894 (mmmm) REVERT: 3 304 GLU cc_start: 0.8699 (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: 0.8103 (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: 0.8463 (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: 0.8692 (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: 0.9086 (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: 0.8743 (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: 0.7567 (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: 0.8875 (OUTLIER) cc_final: 0.8633 (tp30) REVERT: YA 1202 LYS cc_start: 0.9312 (tttm) cc_final: 0.9044 (tttm) REVERT: YA 1204 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8089 (tm-30) REVERT: ZA 1304 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8459 (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: 0.8582 (tppt) REVERT: d 4 GLU cc_start: 0.8527 (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: 0.7600 (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: 0.8814 (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: 0.8179 (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: 0.9014 (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: 0.8359 (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: 0.8371 (tp30) REVERT: NB 102 LYS cc_start: 0.9346 (tptm) cc_final: 0.9118 (pttt) REVERT: NB 103 PHE cc_start: 0.9117 (t80) cc_final: 0.8776 (t80) REVERT: NB 104 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8301 (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: 0.8229 (tp30) REVERT: QB 1006 LYS cc_start: 0.9264 (ttpt) cc_final: 0.8946 (ttpt) REVERT: SB 1204 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8270 (tm-30) outliers start: 131 outliers final: 67 residues processed: 497 average time/residue: 0.1958 time to fit residues: 119.4659 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 : 0.305 ------------------------------------------------------------------------------- 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 are 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 : 0.446 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: 0.7578 (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: 0.8936 (mmmm) REVERT: S 307 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9069 (m-80) REVERT: T 1004 GLU cc_start: 0.8699 (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: 0.8753 (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: 0.8605 (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: 0.8852 (mmmm) REVERT: s 1204 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8465 (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: 0.8959 (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: 0.8101 (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: 0.8438 (mm-30) REVERT: G 4 GLU cc_start: 0.8318 (mp0) cc_final: 0.7752 (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: 0.8110 (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: 0.9033 (ttmt) REVERT: MA 102 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8849 (mmtt) REVERT: PA 1004 GLU cc_start: 0.8338 (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: 0.8925 (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: 0.9290 (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: 0.9172 (OUTLIER) cc_final: 0.8758 (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: 0.9202 (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: 0.7971 (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: 0.7622 (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: 0.9141 (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: 0.9369 (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: 0.8865 (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: 0.8728 (OUTLIER) cc_final: 0.8370 (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: 0.1962 time to fit residues: 122.5604 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 : 0.361 ------------------------------------------------------------------------------- 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 are 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 : 0.482 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: 0.8697 (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: 0.8135 (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: 0.8769 (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: 0.8121 (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: 0.8363 (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: 0.8871 (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: 0.9185 (OUTLIER) cc_final: 0.8833 (t80) REVERT: ZA 1304 GLU cc_start: 0.9205 (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: 0.7893 (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: 0.8338 (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: 0.7943 (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: 0.8239 (tm-30) cc_final: 0.7552 (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: 0.9176 (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: 0.8807 (ttpt) REVERT: vA 104 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8575 (tm-30) REVERT: wA 202 LYS cc_start: 0.9325 (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: 0.9261 (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: 0.8258 (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: 0.8008 (tm-30) cc_final: 0.7449 (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: 0.9041 (tptp) cc_final: 0.8810 (tptp) REVERT: i 4 GLU cc_start: 0.8911 (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: 0.8290 (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: 0.1990 time to fit residues: 126.2818 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 : 0.419 ------------------------------------------------------------------------------- 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 are 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 : 0.427 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: 0.8406 (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: 0.8146 (mm-30) REVERT: Q 106 LYS cc_start: 0.9292 (mmmm) cc_final: 0.8948 (mmmm) REVERT: S 307 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.9107 (m-80) REVERT: T 1004 GLU cc_start: 0.8694 (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: 0.8205 (mm-30) REVERT: U 1106 LYS cc_start: 0.9058 (tptm) cc_final: 0.8655 (tptm) REVERT: W 1302 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9018 (ttmm) REVERT: C 4 GLU cc_start: 0.8540 (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: 0.8740 (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: 0.8649 (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: 0.8646 (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: 0.2887 (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: 0.8518 (tm-30) REVERT: TA 106 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8897 (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: 0.9277 (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: 0.8882 (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: 0.7854 (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: 0.8093 (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: 0.8926 (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: 0.7656 (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: tA 1206 LYS cc_start: 0.9206 (tttt) cc_final: 0.9006 (tmtt) 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: 0.8966 (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: 0.9185 (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: 0.1947 time to fit residues: 125.4675 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 : 0.367 ------------------------------------------------------------------------------- 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 = 0.070696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.060168 restraints weight = 34590.298| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.21 r_work: 0.2648 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.7558 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 : 4.051 30.001 16272 Z= 1.832 Chirality : 0.299 0.972 1152 Planarity : 0.017 0.061 2160 Dihedral : 20.576 82.779 1496 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 107.92 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.44 % Favored : 80.38 % Rotamer: Outliers : 26.74 % Allowed : 23.26 % Favored : 50.00 % Cbeta Deviations : 15.19 % 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 are 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 0.11017 (12528) covalent geometry : angle 4.05086 (16272) hydrogen bonds : bond 0.19117 ( 278) hydrogen bonds : angle 9.47668 ( 786) Misc. bond : bond 0.01081 ( 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 661 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 430 time to evaluate : 0.364 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: A 4 GLU cc_start: 0.8284 (mp0) cc_final: 0.7368 (mp0) REVERT: A 6 LYS cc_start: 0.9314 (mtmt) cc_final: 0.9041 (mtmt) REVERT: J 104 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8168 (mm-30) REVERT: M 1004 GLU cc_start: 0.8440 (mp0) cc_final: 0.7624 (mp0) REVERT: N 1104 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8505 (mm-30) REVERT: N 1106 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8665 (mmmm) REVERT: O 1206 LYS cc_start: 0.9271 (ttmm) cc_final: 0.9069 (ttmm) REVERT: P 1304 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8573 (mm-30) REVERT: B 4 GLU cc_start: 0.8400 (mp0) cc_final: 0.8024 (mp0) REVERT: Q 104 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8278 (mm-30) REVERT: Q 106 LYS cc_start: 0.9284 (mmmm) cc_final: 0.8951 (mmmm) REVERT: S 307 PHE cc_start: 0.9470 (OUTLIER) cc_final: 0.9110 (m-80) REVERT: T 1004 GLU cc_start: 0.8697 (mp0) cc_final: 0.7958 (mp0) REVERT: T 1006 LYS cc_start: 0.9326 (mtmt) cc_final: 0.9022 (mtmt) REVERT: U 1104 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8193 (mm-30) REVERT: U 1106 LYS cc_start: 0.9033 (tptm) cc_final: 0.8661 (tptm) REVERT: W 1302 LYS cc_start: 0.9367 (mtpt) cc_final: 0.9012 (ttmm) REVERT: C 4 GLU cc_start: 0.8544 (mp0) cc_final: 0.7629 (mp0) REVERT: X 106 LYS cc_start: 0.9337 (mmmm) cc_final: 0.8993 (mmmm) REVERT: j 1004 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: j 1006 LYS cc_start: 0.9291 (mtmt) cc_final: 0.8939 (mtmt) REVERT: k 1104 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8237 (mm-30) REVERT: k 1106 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8820 (mmmm) REVERT: l 1202 LYS cc_start: 0.9385 (mtpt) cc_final: 0.9172 (mtpp) REVERT: D 4 GLU cc_start: 0.8398 (mp0) cc_final: 0.7673 (mp0) REVERT: D 6 LYS cc_start: 0.9287 (mtmt) cc_final: 0.8835 (mtmt) REVERT: D 7 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8712 (t80) REVERT: n 106 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8765 (mmmm) REVERT: r 1104 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8072 (mm-30) REVERT: r 1106 LYS cc_start: 0.9181 (mmmm) cc_final: 0.8807 (mmmm) REVERT: E 6 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8944 (mtmt) REVERT: u 106 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8594 (mmmm) REVERT: v 206 LYS cc_start: 0.9441 (ttmm) cc_final: 0.9206 (ttmm) REVERT: w 302 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8989 (mmmm) REVERT: w 307 PHE cc_start: 0.9564 (OUTLIER) cc_final: 0.8836 (m-80) REVERT: x 1006 LYS cc_start: 0.9156 (mtmt) cc_final: 0.8714 (mtmt) REVERT: y 1106 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8951 (mmmm) REVERT: F 6 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8947 (mtmt) REVERT: 1 104 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8175 (mm-30) REVERT: 1 106 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8718 (mmmm) REVERT: 3 302 LYS cc_start: 0.9473 (ttpt) cc_final: 0.9106 (ttmm) REVERT: 5 1104 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8328 (mp0) REVERT: 5 1106 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8728 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9438 (mtpt) cc_final: 0.9073 (mtpp) REVERT: G 3 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: G 4 GLU cc_start: 0.8371 (mp0) cc_final: 0.7953 (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: 0.7933 (mm-30) REVERT: 8 106 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8678 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8548 (mp0) cc_final: 0.8196 (mp0) REVERT: CA 1104 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8216 (mm-30) REVERT: H 4 GLU cc_start: 0.4190 (OUTLIER) cc_final: 0.2846 (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: 0.9037 (mmmm) REVERT: HA 304 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8599 (mm-30) REVERT: JA 1104 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8509 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8801 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9249 (mtpt) cc_final: 0.9039 (pttm) REVERT: I 4 GLU cc_start: 0.8261 (mp0) cc_final: 0.7372 (mp0) REVERT: MA 106 LYS cc_start: 0.4901 (OUTLIER) cc_final: 0.3806 (tptt) REVERT: PA 1004 GLU cc_start: 0.8471 (mp0) cc_final: 0.7822 (mp0) REVERT: RA 1202 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9125 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8569 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9272 (tttt) cc_final: 0.8871 (tttt) REVERT: SA 1307 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.8571 (m-80) REVERT: a 2 LYS cc_start: 0.9261 (tppt) cc_final: 0.9011 (tppt) REVERT: a 4 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8478 (tp30) REVERT: TA 106 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8866 (ptmm) REVERT: UA 202 LYS cc_start: 0.9440 (tttm) cc_final: 0.9029 (ttmm) REVERT: UA 204 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7879 (tm-30) REVERT: VA 302 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9088 (tptp) REVERT: WA 1002 LYS cc_start: 0.9280 (tppt) cc_final: 0.8899 (tppt) REVERT: WA 1004 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8625 (tp30) REVERT: YA 1204 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7858 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8817 (t80) REVERT: ZA 1304 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8601 (tm-30) REVERT: ZA 1306 LYS cc_start: 0.8953 (tptp) cc_final: 0.8685 (tptp) REVERT: b 6 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9032 (ttpt) REVERT: aA 104 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8033 (tm-30) REVERT: bA 202 LYS cc_start: 0.9372 (tttm) cc_final: 0.9043 (ttmm) REVERT: bA 204 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8130 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8964 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9228 (tm-30) cc_final: 0.7818 (tm-30) REVERT: iA 204 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8174 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.9108 (t80) REVERT: nA 1306 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8934 (tptp) REVERT: d 4 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: oA 102 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9076 (tptm) REVERT: pA 204 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7664 (tm-30) REVERT: qA 306 LYS cc_start: 0.9128 (tptp) cc_final: 0.8859 (tptp) REVERT: tA 1204 GLU cc_start: 0.8720 (tm-30) cc_final: 0.7936 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9220 (tttt) cc_final: 0.9014 (tmtt) REVERT: e 4 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8413 (tp30) REVERT: e 6 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8830 (ttpt) REVERT: vA 104 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8572 (tm-30) REVERT: wA 202 LYS cc_start: 0.9345 (tttm) cc_final: 0.8979 (ttmm) REVERT: wA 204 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8277 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8364 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8339 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8598 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.9078 (t80) REVERT: f 2 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8900 (ttmt) REVERT: f 4 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8568 (tp30) REVERT: 3A 202 LYS cc_start: 0.9383 (tttm) cc_final: 0.9114 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8238 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9173 (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: 0.8528 (tm-30) cc_final: 0.8060 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8939 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8329 (tm-30) REVERT: g 2 LYS cc_start: 0.9173 (tppt) cc_final: 0.8676 (tppt) REVERT: g 4 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8389 (tp30) REVERT: AB 202 LYS cc_start: 0.9451 (tttm) cc_final: 0.9110 (ttmm) REVERT: AB 204 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8057 (tm-30) REVERT: BB 302 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9052 (tptp) REVERT: BB 305 PHE cc_start: 0.9497 (OUTLIER) cc_final: 0.9262 (t80) REVERT: CB 1004 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8454 (tp30) REVERT: DB 1102 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9097 (tptm) REVERT: EB 1204 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7563 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9045 (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: 0.9467 (OUTLIER) cc_final: 0.9142 (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: 0.8980 (tptp) REVERT: JB 1004 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8290 (tp30) REVERT: i 4 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8507 (tp30) REVERT: NB 102 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9142 (pttt) REVERT: NB 104 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8307 (pm20) REVERT: NB 106 LYS cc_start: 0.9222 (tttp) cc_final: 0.8699 (pptt) REVERT: OB 202 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9196 (mmmm) REVERT: QB 1004 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8087 (tp30) REVERT: QB 1005 PHE cc_start: 0.9305 (t80) cc_final: 0.8720 (t80) outliers start: 231 outliers final: 165 residues processed: 529 average time/residue: 0.1935 time to fit residues: 126.1782 Evaluate side-chains 638 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 430 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 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 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 = 0.3107 r_free = 0.3107 target = 0.070730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.060247 restraints weight = 34473.400| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.20 r_work: 0.2652 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.7603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.110 0.352 12563 Z= 4.896 Angle : 4.086 30.722 16272 Z= 1.848 Chirality : 0.300 0.967 1152 Planarity : 0.017 0.062 2160 Dihedral : 20.575 83.047 1496 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 108.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 19.97 % Favored : 79.86 % Rotamer: Outliers : 26.85 % Allowed : 23.50 % Favored : 49.65 % Cbeta Deviations : 15.19 % 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 are 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 0.129 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11028 (12528) covalent geometry : angle 4.08631 (16272) hydrogen bonds : bond 0.19098 ( 278) hydrogen bonds : angle 9.48043 ( 786) Misc. bond : bond 0.01100 ( 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 660 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 428 time to evaluate : 0.430 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: A 4 GLU cc_start: 0.8249 (mp0) cc_final: 0.7292 (mp0) REVERT: A 6 LYS cc_start: 0.9314 (mtmt) cc_final: 0.8949 (mtmt) REVERT: J 104 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8147 (mm-30) REVERT: J 106 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.8842 (tmmm) REVERT: M 1004 GLU cc_start: 0.8468 (mp0) cc_final: 0.7525 (mp0) REVERT: N 1104 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8497 (mm-30) REVERT: N 1106 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8654 (mmmm) REVERT: O 1206 LYS cc_start: 0.9260 (ttmm) cc_final: 0.9049 (ttmm) REVERT: P 1304 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8568 (mm-30) REVERT: B 4 GLU cc_start: 0.8396 (mp0) cc_final: 0.8051 (mp0) REVERT: B 5 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.9172 (m-80) REVERT: Q 104 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8265 (mm-30) REVERT: Q 106 LYS cc_start: 0.9267 (mmmm) cc_final: 0.8953 (mmmm) REVERT: T 1004 GLU cc_start: 0.8691 (mp0) cc_final: 0.7968 (mp0) REVERT: T 1006 LYS cc_start: 0.9332 (mtmt) cc_final: 0.9017 (mtmt) REVERT: U 1104 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8191 (mm-30) REVERT: U 1106 LYS cc_start: 0.9027 (tptm) cc_final: 0.8663 (tptm) REVERT: C 4 GLU cc_start: 0.8573 (mp0) cc_final: 0.7642 (mp0) REVERT: X 106 LYS cc_start: 0.9350 (mmmm) cc_final: 0.9008 (mmmm) REVERT: j 1004 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: j 1006 LYS cc_start: 0.9291 (mtmt) cc_final: 0.8945 (mtmt) REVERT: k 1104 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8331 (mm-30) REVERT: k 1106 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8823 (mmmm) REVERT: l 1202 LYS cc_start: 0.9381 (mtpt) cc_final: 0.9141 (mtpp) REVERT: l 1204 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8683 (mm-30) REVERT: D 4 GLU cc_start: 0.8403 (mp0) cc_final: 0.7685 (mp0) REVERT: D 6 LYS cc_start: 0.9288 (mtmt) cc_final: 0.8830 (mtmt) REVERT: D 7 PHE cc_start: 0.9380 (OUTLIER) cc_final: 0.8698 (t80) REVERT: n 106 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8783 (mmmm) REVERT: r 1104 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: r 1106 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8825 (mmmm) REVERT: E 6 LYS cc_start: 0.9200 (mtmt) cc_final: 0.8935 (mtmt) REVERT: u 106 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8598 (mmmm) REVERT: v 206 LYS cc_start: 0.9441 (ttmm) cc_final: 0.9185 (ttmm) REVERT: w 307 PHE cc_start: 0.9550 (OUTLIER) cc_final: 0.8959 (m-80) REVERT: x 1006 LYS cc_start: 0.9146 (mtmt) cc_final: 0.8738 (mtmt) REVERT: y 1106 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8960 (mmmm) REVERT: F 6 LYS cc_start: 0.9273 (mtmt) cc_final: 0.8978 (mtmt) REVERT: 1 104 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8191 (mm-30) REVERT: 1 106 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8725 (mmmm) REVERT: 3 302 LYS cc_start: 0.9483 (ttpt) cc_final: 0.9112 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8802 (mmmm) REVERT: 6 1202 LYS cc_start: 0.9430 (mtpt) cc_final: 0.9059 (mtpp) REVERT: G 3 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7923 (m-80) REVERT: G 4 GLU cc_start: 0.8377 (mp0) cc_final: 0.7988 (mp0) REVERT: G 6 LYS cc_start: 0.9349 (mtmt) cc_final: 0.9025 (mtmt) REVERT: 8 104 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7948 (mm-30) REVERT: 8 106 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8661 (mmmm) REVERT: BA 1004 GLU cc_start: 0.8469 (mp0) cc_final: 0.8059 (mp0) REVERT: CA 1104 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8212 (mm-30) REVERT: H 4 GLU cc_start: 0.4166 (OUTLIER) cc_final: 0.2828 (pm20) REVERT: FA 106 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8987 (mmmm) REVERT: HA 302 LYS cc_start: 0.9346 (mtpt) cc_final: 0.9040 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8269 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8776 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9252 (mtpt) cc_final: 0.9027 (pttp) REVERT: I 4 GLU cc_start: 0.8261 (mp0) cc_final: 0.7396 (mp0) REVERT: MA 106 LYS cc_start: 0.5147 (OUTLIER) cc_final: 0.4441 (tptt) REVERT: PA 1004 GLU cc_start: 0.8464 (mp0) cc_final: 0.7808 (mp0) REVERT: PA 1006 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.9038 (ttmt) REVERT: RA 1202 LYS cc_start: 0.9361 (mtpt) cc_final: 0.9126 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8567 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9274 (tttt) cc_final: 0.8866 (tttt) REVERT: SA 1307 PHE cc_start: 0.9460 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: a 2 LYS cc_start: 0.9268 (tppt) cc_final: 0.9020 (tppt) REVERT: a 4 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8490 (tp30) REVERT: TA 104 GLU cc_start: 0.8932 (tm-30) cc_final: 0.7996 (tm-30) REVERT: TA 106 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8831 (ptmm) REVERT: UA 202 LYS cc_start: 0.9438 (tttm) cc_final: 0.9024 (ttmm) REVERT: UA 204 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7862 (tm-30) REVERT: VA 302 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9087 (tptp) REVERT: WA 1002 LYS cc_start: 0.9264 (tppt) cc_final: 0.8892 (tppt) REVERT: WA 1004 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8633 (tp30) REVERT: YA 1204 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7868 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9237 (OUTLIER) cc_final: 0.8824 (t80) REVERT: ZA 1304 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8591 (tm-30) REVERT: aA 104 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8005 (tm-30) REVERT: bA 202 LYS cc_start: 0.9371 (tttm) cc_final: 0.9040 (ttmm) REVERT: bA 204 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8119 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8964 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9233 (tm-30) cc_final: 0.7843 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9305 (t80) cc_final: 0.8937 (t80) REVERT: c 4 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7862 (tm-30) REVERT: iA 202 LYS cc_start: 0.9448 (tttm) cc_final: 0.9151 (mmmm) REVERT: iA 204 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8221 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9116 (t80) REVERT: nA 1306 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8934 (tptp) REVERT: d 2 LYS cc_start: 0.9199 (tppt) cc_final: 0.8887 (tppt) REVERT: d 4 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8103 (tp30) REVERT: oA 102 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9081 (tptm) REVERT: pA 204 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7650 (tm-30) REVERT: qA 306 LYS cc_start: 0.9136 (tptp) cc_final: 0.8867 (tptp) REVERT: rA 1006 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8965 (ttpt) REVERT: tA 1204 GLU cc_start: 0.8727 (tm-30) cc_final: 0.7924 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9229 (tttt) cc_final: 0.9006 (tmtt) REVERT: e 4 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8382 (tp30) REVERT: e 6 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8839 (ttpt) REVERT: vA 104 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8571 (tm-30) REVERT: wA 202 LYS cc_start: 0.9342 (tttm) cc_final: 0.8968 (ttmm) REVERT: wA 204 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8299 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8335 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8335 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8608 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9370 (OUTLIER) cc_final: 0.9085 (t80) REVERT: f 2 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8899 (ttmt) REVERT: f 4 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8563 (tp30) REVERT: 3A 202 LYS cc_start: 0.9370 (tttm) cc_final: 0.9113 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8180 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8885 (tptp) REVERT: 4A 304 GLU cc_start: 0.9347 (tm-30) cc_final: 0.8432 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8071 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8952 (tptp) REVERT: 8A 1304 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8316 (tm-30) REVERT: g 2 LYS cc_start: 0.9158 (tppt) cc_final: 0.8669 (tppt) REVERT: g 4 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8390 (tp30) REVERT: AB 202 LYS cc_start: 0.9448 (tttm) cc_final: 0.9139 (ttmm) REVERT: AB 204 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8067 (tm-30) REVERT: BB 302 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9056 (tptp) REVERT: BB 305 PHE cc_start: 0.9500 (OUTLIER) cc_final: 0.9275 (t80) REVERT: CB 1004 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8455 (tp30) REVERT: DB 1102 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9100 (tptm) REVERT: EB 1204 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7584 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8734 (tptp) REVERT: h 4 GLU cc_start: 0.8793 (tp30) cc_final: 0.8177 (pm20) REVERT: GB 103 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.9137 (t80) REVERT: HB 202 LYS cc_start: 0.9413 (tttm) cc_final: 0.9047 (pttt) REVERT: IB 306 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8958 (tptp) REVERT: JB 1004 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8299 (tp30) REVERT: i 4 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8534 (tp30) REVERT: NB 102 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9141 (pttt) REVERT: NB 104 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8300 (pm20) REVERT: NB 106 LYS cc_start: 0.9224 (tttp) cc_final: 0.8715 (pptt) REVERT: QB 1004 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8094 (tp30) REVERT: QB 1005 PHE cc_start: 0.9314 (t80) cc_final: 0.8732 (t80) REVERT: QB 1006 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9062 (ttpt) outliers start: 232 outliers final: 168 residues processed: 531 average time/residue: 0.1955 time to fit residues: 128.2812 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 : 0.433 ------------------------------------------------------------------------------- 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 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 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 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 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 = 0.3101 r_free = 0.3101 target = 0.070351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060002 restraints weight = 34426.921| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.18 r_work: 0.2650 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.7634 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= 4.894 Angle : 4.093 30.426 16272 Z= 1.848 Chirality : 0.300 0.968 1152 Planarity : 0.017 0.063 2160 Dihedral : 20.526 83.295 1496 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 108.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.44 % Favored : 80.56 % Rotamer: Outliers : 27.66 % Allowed : 23.61 % Favored : 48.73 % Cbeta Deviations : 15.28 % 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 are 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 0.129 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11025 (12528) covalent geometry : angle 4.09303 (16272) hydrogen bonds : bond 0.19112 ( 278) hydrogen bonds : angle 9.49335 ( 786) Misc. bond : bond 0.01147 ( 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 670 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 431 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8257 (mp0) cc_final: 0.7287 (mp0) REVERT: A 6 LYS cc_start: 0.9308 (mtmt) cc_final: 0.8954 (mtmt) REVERT: J 104 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8195 (mm-30) REVERT: J 106 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8809 (tmmm) REVERT: M 1004 GLU cc_start: 0.8475 (mp0) cc_final: 0.7488 (mp0) REVERT: N 1104 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8481 (mm-30) REVERT: N 1106 LYS cc_start: 0.9117 (mmmm) cc_final: 0.8632 (mmmm) REVERT: O 1206 LYS cc_start: 0.9274 (ttmm) cc_final: 0.9063 (ttmm) REVERT: P 1304 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8611 (mm-30) REVERT: B 4 GLU cc_start: 0.8385 (mp0) cc_final: 0.8052 (mp0) REVERT: Q 104 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8251 (mm-30) REVERT: Q 106 LYS cc_start: 0.9275 (mmmm) cc_final: 0.8960 (mmmm) REVERT: T 1004 GLU cc_start: 0.8694 (mp0) cc_final: 0.7960 (mp0) REVERT: T 1006 LYS cc_start: 0.9323 (mtmt) cc_final: 0.8968 (mtmt) REVERT: U 1104 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8185 (mm-30) REVERT: U 1106 LYS cc_start: 0.9047 (tptm) cc_final: 0.8675 (tptm) REVERT: W 1302 LYS cc_start: 0.9375 (mtpt) cc_final: 0.9034 (mtpp) REVERT: C 4 GLU cc_start: 0.8557 (mp0) cc_final: 0.7621 (mp0) REVERT: X 106 LYS cc_start: 0.9354 (mmmm) cc_final: 0.9012 (mmmm) REVERT: j 1004 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: j 1006 LYS cc_start: 0.9298 (mtmt) cc_final: 0.8890 (mtmt) REVERT: k 1104 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8335 (mm-30) REVERT: k 1106 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8832 (mmmm) REVERT: l 1202 LYS cc_start: 0.9369 (mtpt) cc_final: 0.9122 (mtpp) REVERT: D 4 GLU cc_start: 0.8408 (mp0) cc_final: 0.7713 (mp0) REVERT: D 6 LYS cc_start: 0.9293 (mtmt) cc_final: 0.8844 (mtmt) REVERT: D 7 PHE cc_start: 0.9387 (OUTLIER) cc_final: 0.8709 (t80) REVERT: n 106 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8773 (mmmm) REVERT: o 202 LYS cc_start: 0.9391 (ttpt) cc_final: 0.9070 (ttpt) REVERT: r 1104 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: r 1106 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8758 (mmmm) REVERT: E 6 LYS cc_start: 0.9202 (mtmt) cc_final: 0.8951 (mtmt) REVERT: u 106 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8593 (mmmm) REVERT: v 206 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9204 (ttmm) REVERT: w 302 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8975 (mmmm) REVERT: w 307 PHE cc_start: 0.9580 (OUTLIER) cc_final: 0.9004 (m-80) REVERT: x 1003 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8819 (m-80) REVERT: x 1006 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8737 (mtmt) REVERT: y 1106 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8941 (mmmm) REVERT: F 6 LYS cc_start: 0.9283 (mtmt) cc_final: 0.9005 (mtmt) REVERT: 1 104 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8195 (mm-30) REVERT: 1 106 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8768 (mmmm) REVERT: 3 302 LYS cc_start: 0.9447 (ttpt) cc_final: 0.9151 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8798 (mmmm) REVERT: G 3 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: G 4 GLU cc_start: 0.8378 (mp0) cc_final: 0.8004 (mp0) REVERT: G 6 LYS cc_start: 0.9347 (mtmt) cc_final: 0.9026 (mtmt) REVERT: 8 104 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7942 (mm-30) REVERT: 8 106 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8681 (mmmm) REVERT: CA 1104 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8159 (mm-30) REVERT: H 4 GLU cc_start: 0.4177 (OUTLIER) cc_final: 0.2837 (pm20) REVERT: FA 106 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8991 (mmmm) REVERT: HA 302 LYS cc_start: 0.9374 (mtpt) cc_final: 0.9046 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8249 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8787 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9253 (mtpt) cc_final: 0.9024 (pttp) REVERT: I 4 GLU cc_start: 0.8242 (mp0) cc_final: 0.7405 (mp0) REVERT: MA 106 LYS cc_start: 0.5138 (OUTLIER) cc_final: 0.3857 (tptt) REVERT: PA 1004 GLU cc_start: 0.8470 (mp0) cc_final: 0.7804 (mp0) REVERT: PA 1006 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.9031 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9513 (OUTLIER) cc_final: 0.8919 (m-80) REVERT: RA 1202 LYS cc_start: 0.9362 (mtpt) cc_final: 0.9126 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8554 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9269 (tttt) cc_final: 0.8861 (tttt) REVERT: SA 1307 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.8633 (m-80) REVERT: a 2 LYS cc_start: 0.9266 (tppt) cc_final: 0.9026 (tppt) REVERT: a 4 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8489 (tp30) REVERT: TA 106 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8907 (ptmm) REVERT: UA 202 LYS cc_start: 0.9440 (tttm) cc_final: 0.9031 (ttmm) REVERT: UA 204 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7848 (tm-30) REVERT: VA 302 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9084 (tptp) REVERT: WA 1002 LYS cc_start: 0.9271 (tppt) cc_final: 0.8891 (tppt) REVERT: WA 1004 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8635 (tp30) REVERT: YA 1204 GLU cc_start: 0.8474 (tm-30) cc_final: 0.7870 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.8816 (t80) REVERT: ZA 1304 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8604 (tm-30) REVERT: aA 104 GLU cc_start: 0.8882 (tm-30) cc_final: 0.7988 (tm-30) REVERT: bA 202 LYS cc_start: 0.9373 (tttm) cc_final: 0.9042 (ttmm) REVERT: bA 204 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8125 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8964 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9226 (tm-30) cc_final: 0.7838 (tm-30) REVERT: c 4 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8430 (tp30) REVERT: iA 202 LYS cc_start: 0.9443 (tttm) cc_final: 0.9143 (mmmm) REVERT: iA 204 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8222 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9115 (t80) REVERT: nA 1306 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8934 (tptp) REVERT: d 2 LYS cc_start: 0.9201 (tppt) cc_final: 0.8898 (tppt) REVERT: d 4 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: oA 102 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9090 (tptm) REVERT: pA 204 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7630 (tm-30) REVERT: qA 306 LYS cc_start: 0.9126 (tptp) cc_final: 0.8854 (tptp) REVERT: tA 1204 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8166 (tm-30) REVERT: tA 1206 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.9025 (tmtt) REVERT: e 4 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8386 (tp30) REVERT: e 6 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8846 (ttpt) REVERT: vA 104 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8562 (tm-30) REVERT: wA 202 LYS cc_start: 0.9349 (tttm) cc_final: 0.8981 (ttmm) REVERT: wA 204 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8297 (tm-30) REVERT: yA 1004 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8331 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8351 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8627 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9079 (t80) REVERT: f 2 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8887 (ttmt) REVERT: f 4 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8567 (tp30) REVERT: 3A 202 LYS cc_start: 0.9363 (tttm) cc_final: 0.9108 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8165 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8879 (tptp) REVERT: 4A 304 GLU cc_start: 0.9344 (tm-30) cc_final: 0.8421 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8067 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8950 (tptp) REVERT: g 2 LYS cc_start: 0.9166 (tppt) cc_final: 0.8678 (tppt) REVERT: g 4 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: 9A 105 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.9120 (t80) REVERT: AB 202 LYS cc_start: 0.9456 (tttm) cc_final: 0.9157 (ttmm) REVERT: AB 204 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8063 (tm-30) REVERT: BB 302 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.9051 (tptp) REVERT: BB 305 PHE cc_start: 0.9502 (OUTLIER) cc_final: 0.9272 (t80) REVERT: CB 1004 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: DB 1102 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9095 (tptm) REVERT: EB 1204 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7581 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8735 (tptp) REVERT: h 4 GLU cc_start: 0.8788 (tp30) cc_final: 0.8176 (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: 0.9043 (pttt) REVERT: IB 306 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8954 (tptp) REVERT: JB 1004 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8287 (tp30) REVERT: i 4 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8533 (tp30) REVERT: NB 102 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9145 (pttt) REVERT: NB 104 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8303 (pm20) REVERT: NB 106 LYS cc_start: 0.9227 (tttp) cc_final: 0.8726 (pptt) REVERT: QB 1004 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: QB 1005 PHE cc_start: 0.9313 (t80) cc_final: 0.8726 (t80) REVERT: QB 1006 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9038 (ttpt) outliers start: 239 outliers final: 176 residues processed: 535 average time/residue: 0.1990 time to fit residues: 131.5225 Evaluate side-chains 655 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 431 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 1206 LYS 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 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 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 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 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 = 0.070434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.060133 restraints weight = 34230.671| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.14 r_work: 0.2656 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.7652 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 : 4.078 30.462 16272 Z= 1.844 Chirality : 0.300 0.966 1152 Planarity : 0.017 0.063 2160 Dihedral : 20.486 83.384 1496 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 109.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.49 % Favored : 79.51 % Rotamer: Outliers : 27.89 % Allowed : 23.61 % Favored : 48.50 % Cbeta Deviations : 15.54 % 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 are 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 0.131 0.017 PHE 2 205 Details of bonding type rmsd covalent geometry : bond 0.11029 (12528) covalent geometry : angle 4.07788 (16272) hydrogen bonds : bond 0.19111 ( 278) hydrogen bonds : angle 9.48779 ( 786) Misc. bond : bond 0.01104 ( 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 671 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 430 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8244 (mp0) cc_final: 0.7273 (mp0) REVERT: A 6 LYS cc_start: 0.9303 (mtmt) cc_final: 0.8943 (mtmt) REVERT: J 104 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8204 (mm-30) REVERT: J 106 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8782 (tmmm) REVERT: M 1004 GLU cc_start: 0.8518 (mp0) cc_final: 0.7692 (mp0) REVERT: N 1104 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8495 (mm-30) REVERT: N 1106 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8626 (mmmm) REVERT: O 1206 LYS cc_start: 0.9263 (ttmm) cc_final: 0.9052 (ttmm) REVERT: B 4 GLU cc_start: 0.8396 (mp0) cc_final: 0.8070 (mp0) REVERT: Q 104 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8241 (mm-30) REVERT: Q 106 LYS cc_start: 0.9272 (mmmm) cc_final: 0.8957 (mmmm) REVERT: T 1004 GLU cc_start: 0.8679 (mp0) cc_final: 0.7942 (mp0) REVERT: T 1006 LYS cc_start: 0.9317 (mtmt) cc_final: 0.8941 (mtmt) REVERT: U 1104 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8191 (mm-30) REVERT: U 1106 LYS cc_start: 0.9049 (tptm) cc_final: 0.8674 (tptm) REVERT: W 1302 LYS cc_start: 0.9378 (mtpt) cc_final: 0.9031 (mtpp) REVERT: C 4 GLU cc_start: 0.8559 (mp0) cc_final: 0.7633 (mp0) REVERT: X 106 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9013 (mmmm) REVERT: j 1004 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: j 1006 LYS cc_start: 0.9296 (mtmt) cc_final: 0.8892 (mtmt) REVERT: k 1104 GLU cc_start: 0.8852 (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: 0.9364 (mtpt) cc_final: 0.9042 (mtpp) REVERT: l 1204 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8588 (mm-30) REVERT: D 4 GLU cc_start: 0.8403 (mp0) cc_final: 0.7707 (mp0) REVERT: D 6 LYS cc_start: 0.9293 (mtmt) cc_final: 0.8850 (mtmt) REVERT: D 7 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8707 (t80) REVERT: n 106 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8757 (mmmm) REVERT: o 202 LYS cc_start: 0.9377 (ttpt) cc_final: 0.9058 (ttpt) REVERT: r 1104 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: r 1106 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8743 (mmmm) REVERT: E 6 LYS cc_start: 0.9195 (mtmt) cc_final: 0.8947 (mtmt) REVERT: u 106 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8582 (mmmm) REVERT: v 206 LYS cc_start: 0.9443 (ttmm) cc_final: 0.9180 (ttmm) REVERT: w 307 PHE cc_start: 0.9525 (OUTLIER) cc_final: 0.9073 (m-80) REVERT: x 1003 PHE cc_start: 0.9169 (OUTLIER) cc_final: 0.8834 (m-80) REVERT: x 1006 LYS cc_start: 0.9139 (mtmt) cc_final: 0.8723 (mtmt) REVERT: y 1106 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8942 (mmmm) REVERT: F 6 LYS cc_start: 0.9277 (mtmt) cc_final: 0.9011 (mtmt) REVERT: 1 104 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8197 (mm-30) REVERT: 1 106 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8775 (mmmm) REVERT: 3 302 LYS cc_start: 0.9445 (ttpt) cc_final: 0.9142 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8812 (mmmm) REVERT: G 3 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: G 4 GLU cc_start: 0.8379 (mp0) cc_final: 0.8003 (mp0) REVERT: G 6 LYS cc_start: 0.9347 (mtmt) cc_final: 0.9031 (mtmt) REVERT: 8 104 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7946 (mm-30) REVERT: 8 106 LYS cc_start: 0.9073 (mmmm) cc_final: 0.8667 (mmmm) REVERT: CA 1104 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8124 (mm-30) REVERT: H 4 GLU cc_start: 0.4155 (OUTLIER) cc_final: 0.2834 (pm20) REVERT: FA 106 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8997 (mmmm) REVERT: HA 302 LYS cc_start: 0.9352 (mtpt) cc_final: 0.9052 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8258 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8782 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9252 (mtpt) cc_final: 0.9022 (pttp) REVERT: I 4 GLU cc_start: 0.8236 (mp0) cc_final: 0.7413 (mp0) REVERT: MA 106 LYS cc_start: 0.5144 (OUTLIER) cc_final: 0.4115 (tptt) REVERT: PA 1004 GLU cc_start: 0.8461 (mp0) cc_final: 0.7772 (mp0) REVERT: PA 1006 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.9027 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9520 (OUTLIER) cc_final: 0.8928 (m-80) REVERT: RA 1202 LYS cc_start: 0.9360 (mtpt) cc_final: 0.9119 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8557 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9262 (tttt) cc_final: 0.8860 (tttt) REVERT: SA 1307 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: a 2 LYS cc_start: 0.9259 (tppt) cc_final: 0.9026 (tppt) REVERT: a 4 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8487 (tp30) REVERT: TA 106 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8881 (ptmm) REVERT: UA 202 LYS cc_start: 0.9438 (tttm) cc_final: 0.9030 (ttmm) REVERT: UA 204 GLU cc_start: 0.8204 (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: 0.9261 (tppt) cc_final: 0.8871 (tppt) REVERT: WA 1004 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8632 (tp30) REVERT: YA 1204 GLU cc_start: 0.8470 (tm-30) cc_final: 0.7851 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8821 (t80) REVERT: ZA 1304 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8606 (tm-30) REVERT: aA 104 GLU cc_start: 0.8844 (tm-30) cc_final: 0.7982 (tm-30) REVERT: bA 202 LYS cc_start: 0.9370 (tttm) cc_final: 0.9037 (ttmm) REVERT: bA 204 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8062 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8954 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9227 (tm-30) cc_final: 0.7837 (tm-30) REVERT: iA 202 LYS cc_start: 0.9429 (tttm) cc_final: 0.9128 (mmmm) REVERT: iA 204 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8225 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9113 (t80) REVERT: d 2 LYS cc_start: 0.9197 (tppt) cc_final: 0.8892 (tppt) REVERT: d 4 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8095 (tp30) REVERT: oA 102 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9099 (tptm) REVERT: pA 204 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7625 (tm-30) REVERT: qA 306 LYS cc_start: 0.9126 (tptp) cc_final: 0.8857 (tptp) REVERT: tA 1204 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8151 (tm-30) REVERT: uA 1307 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.9208 (t80) REVERT: e 4 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8410 (tp30) REVERT: e 6 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8828 (ttpt) REVERT: vA 104 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8558 (tm-30) REVERT: wA 202 LYS cc_start: 0.9347 (tttm) cc_final: 0.8977 (ttmm) REVERT: wA 204 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8289 (tm-30) REVERT: wA 206 LYS cc_start: 0.9229 (tmtt) cc_final: 0.8843 (tmtt) REVERT: yA 1004 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8333 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8630 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.9082 (t80) REVERT: f 2 LYS cc_start: 0.9239 (ttmt) cc_final: 0.8886 (ttmt) REVERT: f 4 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8550 (tp30) REVERT: 3A 202 LYS cc_start: 0.9357 (tttm) cc_final: 0.9058 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8147 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8864 (tptp) REVERT: 4A 304 GLU cc_start: 0.9342 (tm-30) cc_final: 0.8434 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8060 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8940 (tptp) REVERT: g 2 LYS cc_start: 0.9165 (tppt) cc_final: 0.8676 (tppt) REVERT: g 4 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8378 (tp30) REVERT: 9A 105 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.9179 (t80) REVERT: AB 202 LYS cc_start: 0.9437 (tttm) cc_final: 0.9144 (ttmm) REVERT: AB 204 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8076 (tm-30) REVERT: BB 302 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.9039 (tptp) REVERT: BB 305 PHE cc_start: 0.9502 (OUTLIER) cc_final: 0.9278 (t80) REVERT: CB 1004 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8467 (tp30) REVERT: DB 1102 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9091 (tptm) REVERT: EB 1204 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7568 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8727 (tptp) REVERT: h 4 GLU cc_start: 0.8774 (tp30) cc_final: 0.8169 (pm20) REVERT: GB 103 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.9143 (t80) REVERT: HB 202 LYS cc_start: 0.9404 (tttm) cc_final: 0.9040 (pttt) REVERT: IB 306 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8936 (tptp) REVERT: JB 1004 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8289 (tp30) REVERT: i 4 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8530 (tp30) REVERT: NB 102 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9144 (pttt) REVERT: NB 104 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8294 (pm20) REVERT: NB 106 LYS cc_start: 0.9222 (tttp) cc_final: 0.8725 (pptt) REVERT: QB 1004 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8049 (tp30) REVERT: QB 1005 PHE cc_start: 0.9310 (t80) cc_final: 0.8721 (t80) REVERT: QB 1006 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9037 (ttpt) outliers start: 241 outliers final: 176 residues processed: 536 average time/residue: 0.1899 time to fit residues: 125.6318 Evaluate side-chains 652 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 430 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 1002 LYS 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 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 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 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 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 = 0.3102 r_free = 0.3102 target = 0.070490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060135 restraints weight = 34347.049| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.16 r_work: 0.2652 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.7669 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= 4.893 Angle : 4.073 30.613 16272 Z= 1.841 Chirality : 0.300 0.967 1152 Planarity : 0.017 0.064 2160 Dihedral : 20.520 83.474 1496 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 109.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.66 % Favored : 79.34 % Rotamer: Outliers : 27.20 % Allowed : 24.42 % Favored : 48.38 % Cbeta Deviations : 15.80 % 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 are not related in a simple way. whole: -5.93 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (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 0.11022 (12528) covalent geometry : angle 4.07281 (16272) hydrogen bonds : bond 0.19218 ( 278) hydrogen bonds : angle 9.49183 ( 786) Misc. bond : bond 0.01118 ( 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 664 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 429 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8251 (mp0) cc_final: 0.7354 (mp0) REVERT: A 6 LYS cc_start: 0.9300 (mtmt) cc_final: 0.8932 (mtmt) REVERT: J 104 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8197 (mm-30) REVERT: J 106 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8751 (tmmm) REVERT: M 1004 GLU cc_start: 0.8324 (mp0) cc_final: 0.7552 (mp0) REVERT: N 1104 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8515 (mm-30) REVERT: N 1106 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8652 (mmmm) REVERT: O 1206 LYS cc_start: 0.9261 (ttmm) cc_final: 0.9052 (ttmm) REVERT: Q 104 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8202 (mm-30) REVERT: Q 106 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8962 (mmmm) REVERT: T 1004 GLU cc_start: 0.8694 (mp0) cc_final: 0.7958 (mp0) REVERT: T 1006 LYS cc_start: 0.9315 (mtmt) cc_final: 0.8891 (mtmt) REVERT: U 1104 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8186 (mm-30) REVERT: U 1106 LYS cc_start: 0.9052 (tptm) cc_final: 0.8679 (tptm) REVERT: W 1302 LYS cc_start: 0.9391 (mtpt) cc_final: 0.9049 (mtpp) REVERT: C 4 GLU cc_start: 0.8564 (mp0) cc_final: 0.7632 (mp0) REVERT: X 106 LYS cc_start: 0.9362 (mmmm) cc_final: 0.9014 (mmmm) REVERT: j 1004 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8132 (mp0) REVERT: j 1006 LYS cc_start: 0.9304 (mtmt) cc_final: 0.8932 (mtmt) REVERT: k 1104 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8351 (mm-30) REVERT: k 1106 LYS cc_start: 0.9139 (mmmm) cc_final: 0.8841 (mmmm) REVERT: l 1202 LYS cc_start: 0.9365 (mtpt) cc_final: 0.9054 (mtpp) REVERT: l 1204 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8701 (mm-30) REVERT: D 4 GLU cc_start: 0.8399 (mp0) cc_final: 0.7723 (mp0) REVERT: D 6 LYS cc_start: 0.9289 (mtmt) cc_final: 0.8852 (mtmt) REVERT: D 7 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.8707 (t80) REVERT: n 106 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8720 (mmmm) REVERT: o 202 LYS cc_start: 0.9391 (ttpt) cc_final: 0.9096 (ttpt) REVERT: r 1104 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7981 (mm-30) REVERT: r 1106 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8737 (mmmm) REVERT: E 6 LYS cc_start: 0.9205 (mtmt) cc_final: 0.8963 (mtmt) REVERT: u 106 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8606 (mmmm) REVERT: v 206 LYS cc_start: 0.9450 (ttmm) cc_final: 0.9189 (ttmm) REVERT: w 302 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8960 (mmmm) REVERT: w 307 PHE cc_start: 0.9576 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: x 1003 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8849 (m-80) REVERT: x 1006 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8765 (mtmt) REVERT: y 1106 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8949 (mmmm) REVERT: F 6 LYS cc_start: 0.9252 (mtmt) cc_final: 0.8983 (mtmt) REVERT: 1 104 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8213 (mm-30) REVERT: 1 106 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8800 (mmmm) REVERT: 3 302 LYS cc_start: 0.9482 (ttpt) cc_final: 0.9165 (ttmm) REVERT: 5 1106 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8806 (mmmm) REVERT: G 3 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: G 4 GLU cc_start: 0.8386 (mp0) cc_final: 0.8007 (mp0) REVERT: G 6 LYS cc_start: 0.9356 (mtmt) cc_final: 0.9047 (mtmt) REVERT: 8 104 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7951 (mm-30) REVERT: 8 106 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8675 (mmmm) REVERT: CA 1104 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8112 (mm-30) REVERT: H 4 GLU cc_start: 0.4169 (OUTLIER) cc_final: 0.2834 (pm20) REVERT: FA 106 LYS cc_start: 0.9245 (mmmm) cc_final: 0.9001 (mmmm) REVERT: HA 302 LYS cc_start: 0.9366 (mtpt) cc_final: 0.9057 (mmmm) REVERT: JA 1104 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8264 (tm-30) REVERT: JA 1106 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8793 (mmmm) REVERT: KA 1202 LYS cc_start: 0.9250 (mtpt) cc_final: 0.9020 (pttp) REVERT: I 4 GLU cc_start: 0.8246 (mp0) cc_final: 0.7429 (mp0) REVERT: MA 106 LYS cc_start: 0.5073 (OUTLIER) cc_final: 0.3887 (tptt) REVERT: PA 1004 GLU cc_start: 0.8438 (mp0) cc_final: 0.7771 (mp0) REVERT: PA 1006 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9049 (ttmt) REVERT: PA 1007 PHE cc_start: 0.9538 (OUTLIER) cc_final: 0.8959 (m-80) REVERT: RA 1202 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9115 (mtpp) REVERT: SA 1304 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8554 (mm-30) REVERT: SA 1306 LYS cc_start: 0.9264 (tttt) cc_final: 0.8858 (tttt) REVERT: SA 1307 PHE cc_start: 0.9491 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: a 2 LYS cc_start: 0.9255 (tppt) cc_final: 0.9031 (tppt) REVERT: a 4 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8494 (tp30) REVERT: TA 106 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8910 (ptmm) REVERT: UA 202 LYS cc_start: 0.9439 (tttm) cc_final: 0.9015 (ttmm) REVERT: UA 204 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7852 (tm-30) REVERT: VA 302 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9086 (tptp) REVERT: WA 1002 LYS cc_start: 0.9267 (tppt) cc_final: 0.8875 (tppt) REVERT: WA 1004 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8634 (tp30) REVERT: YA 1204 GLU cc_start: 0.8477 (tm-30) cc_final: 0.7847 (tm-30) REVERT: ZA 1303 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8822 (t80) REVERT: ZA 1304 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8608 (tm-30) REVERT: aA 104 GLU cc_start: 0.8846 (tm-30) cc_final: 0.7981 (tm-30) REVERT: bA 202 LYS cc_start: 0.9382 (tttm) cc_final: 0.9051 (ttmm) REVERT: bA 204 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8063 (tm-30) REVERT: dA 1002 LYS cc_start: 0.9198 (ttmt) cc_final: 0.8961 (ttmt) REVERT: gA 1304 GLU cc_start: 0.9218 (tm-30) cc_final: 0.7827 (tm-30) REVERT: gA 1305 PHE cc_start: 0.9247 (t80) cc_final: 0.8866 (t80) REVERT: iA 202 LYS cc_start: 0.9433 (tttm) cc_final: 0.9123 (mmmm) REVERT: iA 204 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8223 (tm-30) REVERT: lA 1103 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.9113 (t80) REVERT: d 2 LYS cc_start: 0.9201 (tppt) cc_final: 0.8890 (tppt) REVERT: d 4 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8095 (tp30) REVERT: oA 102 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9106 (tptm) REVERT: pA 204 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7645 (tm-30) REVERT: qA 306 LYS cc_start: 0.9131 (tptp) cc_final: 0.8863 (tptp) REVERT: tA 1204 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8169 (tm-30) REVERT: uA 1307 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.9162 (t80) REVERT: e 4 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8409 (tp30) REVERT: e 6 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8832 (ttpt) REVERT: vA 104 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8560 (tm-30) REVERT: wA 202 LYS cc_start: 0.9343 (tttm) cc_final: 0.8974 (ttmm) REVERT: wA 204 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8289 (tm-30) REVERT: wA 206 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8853 (tmtt) REVERT: yA 1004 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8334 (tp30) REVERT: 0A 1204 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8343 (tm-30) REVERT: 1A 1304 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8631 (tm-30) REVERT: 1A 1305 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.9084 (t80) REVERT: f 2 LYS cc_start: 0.9242 (ttmt) cc_final: 0.8889 (ttmt) REVERT: f 4 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8569 (tp30) REVERT: 3A 202 LYS cc_start: 0.9368 (tttm) cc_final: 0.9067 (mmmm) REVERT: 3A 204 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8152 (tm-30) REVERT: 4A 302 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8847 (tptp) REVERT: 4A 304 GLU cc_start: 0.9348 (tm-30) cc_final: 0.8444 (tm-30) REVERT: 7A 1204 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8055 (tm-30) REVERT: 8A 1302 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.9001 (tptp) REVERT: 8A 1306 LYS cc_start: 0.8873 (tptp) cc_final: 0.8612 (tptp) REVERT: g 2 LYS cc_start: 0.9170 (tppt) cc_final: 0.8680 (tppt) REVERT: g 4 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8379 (tp30) REVERT: 9A 105 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9173 (t80) REVERT: AB 202 LYS cc_start: 0.9442 (tttm) cc_final: 0.9151 (ttmm) REVERT: AB 204 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8072 (tm-30) REVERT: BB 302 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9042 (tptp) REVERT: BB 305 PHE cc_start: 0.9501 (OUTLIER) cc_final: 0.9274 (t80) REVERT: CB 1004 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8472 (tp30) REVERT: DB 1102 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9100 (tptm) REVERT: EB 1204 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7561 (tm-30) REVERT: FB 1302 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8729 (tptp) REVERT: h 4 GLU cc_start: 0.8767 (tp30) cc_final: 0.8168 (pm20) REVERT: GB 103 PHE cc_start: 0.9466 (OUTLIER) cc_final: 0.9136 (t80) REVERT: HB 202 LYS cc_start: 0.9403 (tttm) cc_final: 0.9038 (pttt) REVERT: IB 306 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8893 (tptp) REVERT: JB 1004 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8294 (tp30) REVERT: i 4 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: NB 102 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9146 (pttt) REVERT: NB 104 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8289 (pm20) REVERT: NB 106 LYS cc_start: 0.9226 (tttp) cc_final: 0.8728 (pptt) REVERT: QB 1004 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: QB 1005 PHE cc_start: 0.9302 (t80) cc_final: 0.8708 (t80) REVERT: QB 1006 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9027 (ttpt) outliers start: 235 outliers final: 180 residues processed: 534 average time/residue: 0.1896 time to fit residues: 124.6544 Evaluate side-chains 657 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 429 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 1002 LYS 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 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 d residue 6 LYS 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 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 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 = 0.3102 r_free = 0.3102 target = 0.070505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060141 restraints weight = 34431.725| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.18 r_work: 0.2652 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.7680 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= 4.893 Angle : 4.073 30.646 16272 Z= 1.841 Chirality : 0.300 0.968 1152 Planarity : 0.018 0.072 2160 Dihedral : 20.511 83.503 1496 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 109.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.31 % Favored : 79.69 % Rotamer: Outliers : 27.55 % Allowed : 24.07 % Favored : 48.38 % Cbeta Deviations : 15.80 % 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 are not related in a simple way. whole: -5.93 (0.24), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.51 (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 0.11024 (12528) covalent geometry : angle 4.07313 (16272) hydrogen bonds : bond 0.19238 ( 278) hydrogen bonds : angle 9.49265 ( 786) Misc. bond : bond 0.01104 ( 35) =============================================================================== Job complete usr+sys time: 2836.29 seconds wall clock time: 49 minutes 32.46 seconds (2972.46 seconds total)