Starting phenix.real_space_refine on Fri Aug 22 23:06:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqi_23487/08_2025/7lqi_23487.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqi_23487/08_2025/7lqi_23487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lqi_23487/08_2025/7lqi_23487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqi_23487/08_2025/7lqi_23487.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lqi_23487/08_2025/7lqi_23487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqi_23487/08_2025/7lqi_23487.map" } resolution = 3.5 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= -0.000 sd= 0.000 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 6000 2.51 5 N 1100 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 215 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8400 Number of models: 1 Model: "" Number of chains: 100 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "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: "VB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "WB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "XB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-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 Time building chain proxies: 2.25, per 1000 atoms: 0.27 Number of scatterers: 8400 At special positions: 0 Unit cell: (98.28, 98.28, 64.8, 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 1300 8.00 N 1100 7.00 C 6000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 274.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'I' and resid 6 through 7 removed outlier: 6.912A pdb=" N LYS G 6 " --> pdb=" O PHE I 7 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS E 6 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS C 6 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS A 6 " --> pdb=" O PHE C 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'JA' and resid 102 through 104 removed outlier: 5.642A pdb=" N LYS K 102 " --> pdb=" O PHE Y 103 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE Y 105 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU K 104 " --> pdb=" O PHE Y 105 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE Y 107 " --> pdb=" O GLU K 104 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS K 106 " --> pdb=" O PHE Y 107 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE K 103 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE R 103 " --> pdb=" O GLU k 104 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE k 103 " --> pdb=" O GLU y 104 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE y 103 " --> pdb=" O GLUCA 104 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYSCA 106 " --> pdb=" O PHE y 103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLUQA 104 " --> pdb=" O PHECA 103 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYSQA 106 " --> pdb=" O PHECA 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'KA' and resid 206 through 207 removed outlier: 7.773A pdb=" N PHEKA 207 " --> pdb=" O GLU 6 204 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS 6 206 " --> pdb=" O PHEKA 207 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS s 202 " --> pdb=" O PHE 6 203 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE 6 205 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU s 204 " --> pdb=" O PHE 6 205 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE 6 207 " --> pdb=" O GLU s 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS s 206 " --> pdb=" O PHE 6 207 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS L 202 " --> pdb=" O PHE Z 203 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE Z 205 " --> pdb=" O LYS L 202 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU L 204 " --> pdb=" O PHE Z 205 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE Z 207 " --> pdb=" O GLU L 204 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS L 206 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE L 203 " --> pdb=" O GLU S 204 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS S 206 " --> pdb=" O PHE L 203 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE L 205 " --> pdb=" O LYS S 206 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE z 203 " --> pdb=" O GLUDA 204 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYSDA 206 " --> pdb=" O PHE z 203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLURA 204 " --> pdb=" O PHEDA 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYSRA 206 " --> pdb=" O PHEDA 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'KA' and resid 206 through 207 removed outlier: 7.773A pdb=" N PHEKA 207 " --> pdb=" O GLU 6 204 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS 6 206 " --> pdb=" O PHEKA 207 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS s 202 " --> pdb=" O PHE 6 203 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE 6 205 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU s 204 " --> pdb=" O PHE 6 205 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE 6 207 " --> pdb=" O GLU s 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS s 206 " --> pdb=" O PHE 6 207 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS L 202 " --> pdb=" O PHE Z 203 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE Z 205 " --> pdb=" O LYS L 202 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU L 204 " --> pdb=" O PHE Z 205 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE Z 207 " --> pdb=" O GLU L 204 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS L 206 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE L 203 " --> pdb=" O GLU S 204 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS S 206 " --> pdb=" O PHE L 203 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE L 205 " --> pdb=" O LYS S 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLURA 204 " --> pdb=" O PHEDA 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYSRA 206 " --> pdb=" O PHEDA 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LA' and resid 302 through 307 removed outlier: 6.205A pdb=" N LYS 7 302 " --> pdb=" O PHELA 303 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHELA 305 " --> pdb=" O LYS 7 302 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU 7 304 " --> pdb=" O PHELA 305 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHELA 307 " --> pdb=" O GLU 7 304 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS 7 306 " --> pdb=" O PHELA 307 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS t 302 " --> pdb=" O PHE 7 303 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE 7 305 " --> pdb=" O LYS t 302 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU t 304 " --> pdb=" O PHE 7 305 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE 7 307 " --> pdb=" O GLU t 304 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS t 306 " --> pdb=" O PHE 7 307 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LYS M 302 " --> pdb=" O PHE f 303 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE f 305 " --> pdb=" O LYS M 302 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU M 304 " --> pdb=" O PHE f 305 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE f 307 " --> pdb=" O GLU M 304 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS M 306 " --> pdb=" O PHE f 307 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE M 303 " --> pdb=" O GLU T 304 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LYS T 306 " --> pdb=" O PHE M 303 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE M 305 " --> pdb=" O LYS T 306 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE 0 303 " --> pdb=" O GLUEA 304 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYSEA 306 " --> pdb=" O PHE 0 303 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE 0 305 " --> pdb=" O LYSEA 306 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHEEA 303 " --> pdb=" O GLUSA 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'MA' and resid 402 through 403 removed outlier: 6.357A pdb=" N LYS 8 402 " --> pdb=" O PHEMA 403 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS u 402 " --> pdb=" O PHE 8 403 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS g 402 " --> pdb=" O PHE u 403 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS N 402 " --> pdb=" O PHE g 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'MA' and resid 406 through 407 removed outlier: 6.747A pdb=" N LYS 8 406 " --> pdb=" O PHEMA 407 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS u 406 " --> pdb=" O PHE 8 407 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS g 406 " --> pdb=" O PHE u 407 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS N 406 " --> pdb=" O PHE g 407 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.791A pdb=" N LYS C 2 " --> pdb=" O PHE E 3 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS E 2 " --> pdb=" O PHE G 3 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS G 2 " --> pdb=" O PHE I 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'd' and resid 5 through 6 removed outlier: 3.743A pdb=" N LYS b 6 " --> pdb=" O GLUGB 54 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS a 6 " --> pdb=" O GLUmA 54 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS c 6 " --> pdb=" O GLUXA 54 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSXA 56 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE1A 55 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS e 6 " --> pdb=" O GLU1A 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'HB' and resid 105 through 106 removed outlier: 3.686A pdb=" N LYSnA 106 " --> pdb=" O GLUIB 154 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYSYA 106 " --> pdb=" O GLUoA 154 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS2A 106 " --> pdb=" O GLUZA 154 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYSWB 106 " --> pdb=" O GLU3A 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'JB' and resid 205 through 206 removed outlier: 3.810A pdb=" N PHEKB 253 " --> pdb=" O PHEJB 205 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSpA 206 " --> pdb=" O GLUKB 254 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYSKB 256 " --> pdb=" O GLUpA 204 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHEqA 255 " --> pdb=" O PHEpA 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHEqA 253 " --> pdb=" O PHEpA 205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYSqA 256 " --> pdb=" O GLUaA 204 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHEbA 255 " --> pdb=" O PHEaA 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHEbA 253 " --> pdb=" O PHEaA 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYSbA 256 " --> pdb=" O GLU4A 204 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE5A 255 " --> pdb=" O PHE4A 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE5A 253 " --> pdb=" O PHE4A 205 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSYB 206 " --> pdb=" O GLU5A 254 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS5A 256 " --> pdb=" O GLUYB 204 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHEZB 253 " --> pdb=" O PHEYB 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LB' and resid 305 through 306 removed outlier: 3.555A pdb=" N PHEMB 353 " --> pdb=" O PHELB 305 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYSrA 306 " --> pdb=" O GLUMB 354 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSMB 356 " --> pdb=" O GLUrA 304 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHEsA 355 " --> pdb=" O PHErA 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHEsA 353 " --> pdb=" O PHErA 305 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYScA 306 " --> pdb=" O GLUsA 354 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHEdA 355 " --> pdb=" O PHEcA 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHEdA 353 " --> pdb=" O PHEcA 305 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS6A 306 " --> pdb=" O GLUdA 354 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE7A 355 " --> pdb=" O PHE6A 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE7A 353 " --> pdb=" O PHE6A 305 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU7A 354 " --> pdb=" O LYSaB 306 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYSaB 306 " --> pdb=" O GLU7A 354 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHEbB 353 " --> pdb=" O PHEaB 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'NB' and resid 405 through 406 removed outlier: 3.651A pdb=" N LYStA 406 " --> pdb=" O GLUOB 454 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSeA 406 " --> pdb=" O GLUuA 454 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS8A 406 " --> pdb=" O GLUfA 454 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYScB 406 " --> pdb=" O GLU9A 454 " (cutoff:3.500A) 152 hydrogen bonds defined for protein. 381 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: 1.28 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 994 1.25 - 1.33: 736 1.33 - 1.40: 2770 1.40 - 1.47: 900 1.47 - 1.54: 3300 Bond restraints: 8700 Sorted by residual: bond pdb=" N 5CRpA 201 " pdb=" CAL 5CRpA 201 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N 5CRaA 201 " pdb=" CAL 5CRaA 201 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N 5CRHB 101 " pdb=" CAL 5CRHB 101 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N 5CR8A 401 " pdb=" CAL 5CR8A 401 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" N 5CRnA 101 " pdb=" CAL 5CRnA 101 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.12e+01 ... (remaining 8695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9967 1.87 - 3.74: 949 3.74 - 5.61: 295 5.61 - 7.48: 20 7.48 - 9.35: 69 Bond angle restraints: 11300 Sorted by residual: angle pdb=" CA 5CR U 401 " pdb=" N 5CR U 401 " pdb=" CAL 5CR U 401 " ideal model delta sigma weight residual 125.23 115.88 9.35 3.00e+00 1.11e-01 9.70e+00 angle pdb=" CA 5CR u 401 " pdb=" N 5CR u 401 " pdb=" CAL 5CR u 401 " ideal model delta sigma weight residual 125.23 115.89 9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" CA 5CR n 401 " pdb=" N 5CR n 401 " pdb=" CAL 5CR n 401 " ideal model delta sigma weight residual 125.23 115.90 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA 5CRFA 401 " pdb=" N 5CRFA 401 " pdb=" CAL 5CRFA 401 " ideal model delta sigma weight residual 125.23 115.90 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA 5CRMA 401 " pdb=" N 5CRMA 401 " pdb=" CAL 5CRMA 401 " ideal model delta sigma weight residual 125.23 115.90 9.33 3.00e+00 1.11e-01 9.67e+00 ... (remaining 11295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 3570 16.29 - 32.58: 425 32.58 - 48.87: 145 48.87 - 65.15: 125 65.15 - 81.44: 35 Dihedral angle restraints: 4300 sinusoidal: 2000 harmonic: 2300 Sorted by residual: dihedral pdb=" CA PHEaA 205 " pdb=" C PHEaA 205 " pdb=" N LYSaA 206 " pdb=" CA LYSaA 206 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHEJB 205 " pdb=" C PHEJB 205 " pdb=" N LYSJB 206 " pdb=" CA LYSJB 206 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHEYB 205 " pdb=" C PHEYB 205 " pdb=" N LYSYB 206 " pdb=" CA LYSYB 206 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 4297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.014: 229 0.014 - 0.029: 321 0.029 - 0.043: 198 0.043 - 0.057: 42 0.057 - 0.072: 10 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA GLU 1 404 " pdb=" N GLU 1 404 " pdb=" C GLU 1 404 " pdb=" CB GLU 1 404 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.28e-01 chirality pdb=" CA GLU n 404 " pdb=" N GLU n 404 " pdb=" C GLU n 404 " pdb=" CB GLU n 404 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.25e-01 chirality pdb=" CA GLU N 404 " pdb=" N GLU N 404 " pdb=" C GLU N 404 " pdb=" CB GLU N 404 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.21e-01 ... (remaining 797 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEpA 205 " -0.007 2.00e-02 2.50e+03 7.22e-03 9.11e-01 pdb=" CG PHEpA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEpA 205 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEpA 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEpA 205 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHEpA 205 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHEpA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEJB 205 " -0.007 2.00e-02 2.50e+03 7.08e-03 8.78e-01 pdb=" CG PHEJB 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEJB 205 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEJB 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEJB 205 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHEJB 205 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHEJB 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE4A 205 " -0.007 2.00e-02 2.50e+03 7.05e-03 8.71e-01 pdb=" CG PHE4A 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE4A 205 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE4A 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE4A 205 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE4A 205 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE4A 205 " -0.002 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2545 2.77 - 3.31: 6509 3.31 - 3.84: 13602 3.84 - 4.37: 17423 4.37 - 4.90: 28904 Nonbonded interactions: 68983 Sorted by model distance: nonbonded pdb=" OE1 GMAcB 408 " pdb=" N2 GMAcB 408 " model vdw 2.242 3.120 nonbonded pdb=" OE1 GMAeA 408 " pdb=" N2 GMAeA 408 " model vdw 2.242 3.120 nonbonded pdb=" OE1 GMAtA 408 " pdb=" N2 GMAtA 408 " model vdw 2.243 3.120 nonbonded pdb=" OE1 GMANB 408 " pdb=" N2 GMANB 408 " model vdw 2.243 3.120 nonbonded pdb=" OE1 GMA8A 408 " pdb=" N2 GMA8A 408 " model vdw 2.243 3.120 ... (remaining 68978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '1A' selection = chain '2A' selection = chain '3A' 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 '9A' selection = chain 'A' selection = chain 'B' 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 'GB' selection = chain 'H' selection = chain 'HB' selection = chain 'I' 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 'NB' selection = chain 'OB' 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 'VB' selection = chain 'WB' selection = chain 'XA' selection = chain 'XB' selection = chain 'Y' selection = chain 'YA' selection = chain 'YB' selection = chain 'Z' selection = chain 'ZA' selection = chain 'ZB' 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 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'oA' selection = chain 'pA' 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 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.016 0.112 8700 Z= 0.771 Angle : 1.399 9.345 11300 Z= 0.568 Chirality : 0.027 0.072 800 Planarity : 0.002 0.007 1500 Dihedral : 20.423 81.443 2700 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 8.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEpA 205 Details of bonding type rmsd covalent geometry : bond 0.01568 ( 8700) covalent geometry : angle 1.39925 (11300) hydrogen bonds : bond 0.35290 ( 139) hydrogen bonds : angle 13.44959 ( 381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 368 time to evaluate : 0.388 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: M 302 LYS cc_start: 0.8276 (tttt) cc_final: 0.7660 (tttm) REVERT: N 404 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6945 (mm-30) REVERT: B 2 LYS cc_start: 0.8999 (tttt) cc_final: 0.8790 (ttmm) REVERT: B 4 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: S 202 LYS cc_start: 0.9090 (tttt) cc_final: 0.8886 (ttmt) REVERT: U 402 LYS cc_start: 0.9254 (tttt) cc_final: 0.9045 (ttmm) REVERT: U 404 GLU cc_start: 0.7725 (mm-30) cc_final: 0.6851 (mt-10) REVERT: C 2 LYS cc_start: 0.8944 (tttt) cc_final: 0.8666 (tttm) REVERT: C 4 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: C 6 LYS cc_start: 0.8693 (tttt) cc_final: 0.8425 (tttp) REVERT: g 406 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8330 (tttp) REVERT: l 204 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: m 302 LYS cc_start: 0.9180 (tttt) cc_final: 0.8905 (ttmt) REVERT: E 4 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: t 302 LYS cc_start: 0.9052 (tttt) cc_final: 0.8815 (ttmm) REVERT: u 402 LYS cc_start: 0.9187 (tttt) cc_final: 0.8774 (ttmm) REVERT: F 2 LYS cc_start: 0.9203 (tttt) cc_final: 0.8897 (tttm) REVERT: y 106 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8723 (tttm) REVERT: 0 304 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7420 (mt-10) REVERT: 1 406 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8652 (ttpt) REVERT: 5 104 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8142 (tm-30) REVERT: 6 204 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: 8 402 LYS cc_start: 0.9116 (tttt) cc_final: 0.8904 (tttp) REVERT: 8 404 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7144 (mt-10) REVERT: H 6 LYS cc_start: 0.8646 (tttt) cc_final: 0.8276 (tptt) REVERT: I 4 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: XA 53 PHE cc_start: 0.7733 (t80) cc_final: 0.7514 (t80) REVERT: XA 56 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8355 (tmtt) REVERT: YA 105 PHE cc_start: 0.8199 (t80) cc_final: 0.7996 (t80) REVERT: ZA 156 LYS cc_start: 0.8788 (tmtt) cc_final: 0.8462 (tmtt) REVERT: aA 206 LYS cc_start: 0.9027 (tttm) cc_final: 0.8764 (tttp) REVERT: bA 257 PHE cc_start: 0.7440 (t80) cc_final: 0.7230 (t80) REVERT: cA 302 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8056 (tmtt) REVERT: dA 352 LYS cc_start: 0.8915 (tmtt) cc_final: 0.8684 (tmtt) REVERT: eA 406 LYS cc_start: 0.9333 (tttp) cc_final: 0.9115 (tttp) REVERT: fA 456 LYS cc_start: 0.8801 (tmtt) cc_final: 0.8472 (tmtt) REVERT: mA 56 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8438 (tptp) REVERT: oA 154 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8011 (tm-30) REVERT: oA 156 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8418 (tptp) REVERT: qA 254 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8044 (tm-30) REVERT: rA 302 LYS cc_start: 0.8806 (tmtt) cc_final: 0.8484 (tmtt) REVERT: sA 354 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8060 (tm-30) REVERT: sA 356 LYS cc_start: 0.8669 (tmtt) cc_final: 0.8441 (tmtt) REVERT: tA 406 LYS cc_start: 0.9404 (tttp) cc_final: 0.9192 (tttm) REVERT: uA 456 LYS cc_start: 0.8623 (tmtt) cc_final: 0.8334 (tmtt) REVERT: 3A 152 LYS cc_start: 0.8829 (tmtt) cc_final: 0.8615 (tmtt) REVERT: 5A 256 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8288 (tmtt) REVERT: 7A 352 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8611 (tmtt) REVERT: 7A 356 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8294 (tmtt) REVERT: GB 52 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8658 (tmtt) REVERT: GB 56 LYS cc_start: 0.8880 (tmtt) cc_final: 0.8650 (tmtt) REVERT: HB 107 PHE cc_start: 0.9122 (t80) cc_final: 0.8172 (t80) REVERT: JB 207 PHE cc_start: 0.9068 (t80) cc_final: 0.8360 (t80) REVERT: KB 256 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8484 (tmtt) REVERT: LB 302 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8360 (ttmm) REVERT: LB 305 PHE cc_start: 0.8372 (t80) cc_final: 0.8169 (t80) REVERT: MB 353 PHE cc_start: 0.7755 (t80) cc_final: 0.7514 (t80) REVERT: MB 356 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8472 (tmtt) REVERT: OB 452 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8586 (tmtt) REVERT: OB 456 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8582 (tmtt) REVERT: ZB 256 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8675 (tmtt) outliers start: 30 outliers final: 4 residues processed: 373 average time/residue: 0.2004 time to fit residues: 88.2688 Evaluate side-chains 340 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 330 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain z residue 204 GLU Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain I residue 4 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.075629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068076 restraints weight = 23891.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.069826 restraints weight = 9321.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.070999 restraints weight = 4814.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071826 restraints weight = 2851.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072405 restraints weight = 1889.348| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.224 8700 Z= 2.321 Angle : 2.721 17.844 11300 Z= 1.297 Chirality : 0.136 0.319 800 Planarity : 0.012 0.039 1500 Dihedral : 26.959 89.476 1030 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 115.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.00 % Favored : 82.00 % Rotamer: Outliers : 16.33 % Allowed : 24.00 % Favored : 59.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.94 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.088 0.012 PHEaA 203 Details of bonding type rmsd covalent geometry : bond 0.05113 ( 8700) covalent geometry : angle 2.72145 (11300) hydrogen bonds : bond 0.13270 ( 139) hydrogen bonds : angle 8.44918 ( 381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 323 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: A 6 LYS cc_start: 0.9076 (tttt) cc_final: 0.8688 (tttm) REVERT: A 7 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: K 104 GLU cc_start: 0.8605 (mp0) cc_final: 0.8258 (mp0) REVERT: K 107 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: L 207 PHE cc_start: 0.9203 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: M 306 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8631 (tttt) REVERT: M 307 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8060 (m-10) REVERT: B 4 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: T 306 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8720 (ttmt) REVERT: C 4 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8538 (mp0) REVERT: C 6 LYS cc_start: 0.8976 (tttt) cc_final: 0.8624 (tttm) REVERT: D 4 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7850 (tm-30) REVERT: m 304 GLU cc_start: 0.8638 (mp0) cc_final: 0.7884 (mp0) REVERT: n 404 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7959 (mt-10) REVERT: E 4 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: E 6 LYS cc_start: 0.9070 (tttt) cc_final: 0.8727 (tttp) REVERT: r 104 GLU cc_start: 0.8596 (mp0) cc_final: 0.8220 (mp0) REVERT: u 404 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7943 (mm-30) REVERT: u 406 LYS cc_start: 0.8972 (mptt) cc_final: 0.8586 (ttmt) REVERT: F 4 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: F 7 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8319 (m-10) REVERT: y 104 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7753 (tm-30) REVERT: y 107 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: z 207 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8197 (m-10) REVERT: 0 307 PHE cc_start: 0.9368 (OUTLIER) cc_final: 0.8580 (m-80) REVERT: G 6 LYS cc_start: 0.9369 (tttt) cc_final: 0.8796 (tttm) REVERT: G 7 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: 6 207 PHE cc_start: 0.9185 (OUTLIER) cc_final: 0.8072 (m-10) REVERT: 7 307 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: H 4 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7546 (tm-30) REVERT: H 6 LYS cc_start: 0.9346 (tttt) cc_final: 0.8936 (ttmt) REVERT: I 6 LYS cc_start: 0.9109 (tttt) cc_final: 0.8780 (tttm) REVERT: KA 204 GLU cc_start: 0.8545 (mp0) cc_final: 0.8337 (pm20) REVERT: LA 304 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8324 (pm20) REVERT: QA 104 GLU cc_start: 0.8868 (pm20) cc_final: 0.8584 (pm20) REVERT: RA 204 GLU cc_start: 0.8890 (pm20) cc_final: 0.8580 (pm20) REVERT: SA 304 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8384 (mp0) REVERT: TA 404 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7582 (tm-30) REVERT: XA 55 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7784 (t80) REVERT: XA 56 LYS cc_start: 0.9132 (tmtt) cc_final: 0.8903 (tttm) REVERT: ZA 155 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7986 (t80) REVERT: ZA 156 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9050 (tmtt) REVERT: aA 203 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.6855 (t80) REVERT: aA 204 GLU cc_start: 0.8392 (tp30) cc_final: 0.7885 (tm-30) REVERT: aA 206 LYS cc_start: 0.9155 (tttm) cc_final: 0.8896 (tttp) REVERT: bA 255 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7783 (t80) REVERT: bA 256 LYS cc_start: 0.9161 (tmtt) cc_final: 0.8941 (tmtt) REVERT: cA 302 LYS cc_start: 0.9111 (tmtt) cc_final: 0.8799 (tmtt) REVERT: cA 303 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.6373 (t80) REVERT: cA 304 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: dA 355 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7630 (t80) REVERT: dA 356 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8694 (tttm) REVERT: eA 406 LYS cc_start: 0.9383 (tttp) cc_final: 0.9158 (tttp) REVERT: fA 455 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8011 (t80) REVERT: fA 456 LYS cc_start: 0.9387 (tmtt) cc_final: 0.9136 (tttm) REVERT: b 2 LYS cc_start: 0.9222 (ttmm) cc_final: 0.8999 (ttmm) REVERT: mA 55 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7245 (t80) REVERT: mA 56 LYS cc_start: 0.9345 (tmtt) cc_final: 0.9129 (tttp) REVERT: oA 155 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7170 (t80) REVERT: oA 156 LYS cc_start: 0.9342 (tmtt) cc_final: 0.9051 (tttp) REVERT: pA 204 GLU cc_start: 0.8578 (tp30) cc_final: 0.8246 (tm-30) REVERT: qA 255 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.6842 (t80) REVERT: rA 302 LYS cc_start: 0.9144 (tmtt) cc_final: 0.8920 (tmtt) REVERT: rA 304 GLU cc_start: 0.8538 (tp30) cc_final: 0.8311 (tp30) REVERT: sA 355 PHE cc_start: 0.8179 (OUTLIER) cc_final: 0.6797 (t80) REVERT: tA 406 LYS cc_start: 0.9336 (tttp) cc_final: 0.8942 (tttp) REVERT: uA 455 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7205 (t80) REVERT: uA 456 LYS cc_start: 0.9396 (tmtt) cc_final: 0.9115 (tttp) REVERT: c 4 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8398 (tm-30) REVERT: 1A 56 LYS cc_start: 0.9325 (tmtt) cc_final: 0.9061 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8314 (tm-30) REVERT: 3A 152 LYS cc_start: 0.9184 (tmtt) cc_final: 0.8882 (tmtt) REVERT: 3A 156 LYS cc_start: 0.9356 (tmtt) cc_final: 0.9034 (tmtt) REVERT: 4A 206 LYS cc_start: 0.9060 (tttm) cc_final: 0.8760 (tttm) REVERT: 5A 256 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8892 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9339 (tmtt) cc_final: 0.8664 (tmtt) REVERT: d 5 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8498 (t80) REVERT: GB 56 LYS cc_start: 0.9340 (tmtt) cc_final: 0.9004 (tmtt) REVERT: HB 105 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8519 (t80) REVERT: LB 302 LYS cc_start: 0.9191 (tmtt) cc_final: 0.8806 (ttmm) REVERT: OB 456 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9168 (tmtt) REVERT: e 4 GLU cc_start: 0.8693 (tp30) cc_final: 0.8248 (tm-30) REVERT: VB 55 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7756 (t80) REVERT: XB 157 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7783 (t80) REVERT: YB 204 GLU cc_start: 0.8590 (tp30) cc_final: 0.8228 (tm-30) REVERT: aB 302 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8665 (tmtt) REVERT: cB 402 LYS cc_start: 0.9155 (tmtt) cc_final: 0.8745 (ttmm) outliers start: 98 outliers final: 40 residues processed: 351 average time/residue: 0.1860 time to fit residues: 77.8445 Evaluate side-chains 388 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 312 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain 7 residue 307 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain SA residue 304 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 405 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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 = 0.3309 r_free = 0.3309 target = 0.076540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068892 restraints weight = 23858.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070654 restraints weight = 9647.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071832 restraints weight = 5036.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072642 restraints weight = 3048.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073226 restraints weight = 2052.999| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.177 8700 Z= 2.312 Angle : 2.728 17.108 11300 Z= 1.309 Chirality : 0.136 0.331 800 Planarity : 0.011 0.040 1500 Dihedral : 26.866 88.323 1021 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 120.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.00 % Favored : 77.00 % Rotamer: Outliers : 18.33 % Allowed : 29.50 % Favored : 52.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.13 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.094 0.011 PHEaA 203 Details of bonding type rmsd covalent geometry : bond 0.05101 ( 8700) covalent geometry : angle 2.72792 (11300) hydrogen bonds : bond 0.12756 ( 139) hydrogen bonds : angle 8.48670 ( 381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 316 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: A 6 LYS cc_start: 0.9088 (tttt) cc_final: 0.8724 (tttm) REVERT: A 7 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: K 104 GLU cc_start: 0.8617 (mp0) cc_final: 0.8409 (mp0) REVERT: K 107 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: L 207 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: M 306 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8713 (ttpt) REVERT: M 307 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8133 (m-10) REVERT: B 4 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: C 4 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8541 (mp0) REVERT: C 6 LYS cc_start: 0.9088 (tttt) cc_final: 0.8712 (tttm) REVERT: k 104 GLU cc_start: 0.8832 (mp0) cc_final: 0.8611 (mp0) REVERT: E 4 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: E 6 LYS cc_start: 0.9039 (tttt) cc_final: 0.8758 (tttp) REVERT: r 104 GLU cc_start: 0.8655 (mp0) cc_final: 0.8357 (mp0) REVERT: u 404 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7807 (mm-30) REVERT: u 406 LYS cc_start: 0.9037 (mptt) cc_final: 0.8597 (ttmt) REVERT: F 7 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.8293 (m-10) REVERT: y 107 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: z 206 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8858 (ttpt) REVERT: z 207 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8228 (m-10) REVERT: 0 307 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.8623 (m-80) REVERT: 1 404 GLU cc_start: 0.8868 (mp0) cc_final: 0.8620 (mp0) REVERT: G 6 LYS cc_start: 0.9437 (tttt) cc_final: 0.8876 (tttm) REVERT: G 7 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.7877 (m-10) REVERT: 6 206 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8775 (ttpt) REVERT: 6 207 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8093 (m-10) REVERT: H 4 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7763 (tm-30) REVERT: H 6 LYS cc_start: 0.9336 (tttt) cc_final: 0.8895 (ttmt) REVERT: I 4 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: I 6 LYS cc_start: 0.9046 (tttt) cc_final: 0.8741 (tttm) REVERT: KA 204 GLU cc_start: 0.8651 (mp0) cc_final: 0.8397 (pm20) REVERT: J 4 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7772 (tm-30) REVERT: QA 104 GLU cc_start: 0.8858 (pm20) cc_final: 0.8455 (pm20) REVERT: RA 204 GLU cc_start: 0.8984 (pm20) cc_final: 0.8674 (pm20) REVERT: SA 304 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: TA 404 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7838 (tm-30) REVERT: a 4 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: XA 55 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7888 (t80) REVERT: XA 56 LYS cc_start: 0.9224 (tmtt) cc_final: 0.8913 (tttp) REVERT: YA 104 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: ZA 155 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7944 (t80) REVERT: ZA 156 LYS cc_start: 0.9410 (tmtt) cc_final: 0.9173 (tttm) REVERT: aA 206 LYS cc_start: 0.9162 (tttm) cc_final: 0.8440 (tttp) REVERT: bA 255 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7775 (t80) REVERT: bA 256 LYS cc_start: 0.9264 (tmtt) cc_final: 0.8944 (tmtt) REVERT: cA 303 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.6704 (t80) REVERT: cA 304 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: dA 355 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7661 (t80) REVERT: dA 356 LYS cc_start: 0.9202 (tmtt) cc_final: 0.8851 (tttp) REVERT: eA 403 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.7386 (t80) REVERT: eA 406 LYS cc_start: 0.9410 (tttp) cc_final: 0.9202 (tttp) REVERT: fA 455 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.8059 (t80) REVERT: fA 456 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9071 (tttp) REVERT: mA 55 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7245 (t80) REVERT: mA 56 LYS cc_start: 0.9392 (tmtt) cc_final: 0.9137 (tttp) REVERT: oA 156 LYS cc_start: 0.9335 (tmtt) cc_final: 0.9122 (tttp) REVERT: sA 355 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.6897 (t80) REVERT: sA 356 LYS cc_start: 0.9091 (tmtt) cc_final: 0.8795 (tttm) REVERT: uA 455 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.6880 (t80) REVERT: uA 456 LYS cc_start: 0.9393 (tmtt) cc_final: 0.9069 (tttp) REVERT: c 4 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: 1A 56 LYS cc_start: 0.9389 (tmtt) cc_final: 0.9058 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8455 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9331 (tmtt) cc_final: 0.8953 (tmtt) REVERT: 4A 204 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7734 (tm-30) REVERT: 4A 206 LYS cc_start: 0.9153 (tttm) cc_final: 0.8886 (tttm) REVERT: 7A 356 LYS cc_start: 0.9368 (tmtt) cc_final: 0.8831 (tmtt) REVERT: d 5 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8360 (t80) REVERT: GB 56 LYS cc_start: 0.9340 (tmtt) cc_final: 0.9119 (tmtt) REVERT: HB 105 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8303 (t80) REVERT: JB 204 GLU cc_start: 0.8614 (tp30) cc_final: 0.8187 (pm20) REVERT: KB 256 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8803 (tmtt) REVERT: LB 302 LYS cc_start: 0.9179 (tmtt) cc_final: 0.8808 (ttmm) REVERT: LB 305 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8302 (t80) REVERT: OB 456 LYS cc_start: 0.9333 (tmtt) cc_final: 0.9115 (tttm) REVERT: VB 55 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.7717 (t80) REVERT: XB 155 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7766 (t80) REVERT: XB 157 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7520 (t80) REVERT: YB 204 GLU cc_start: 0.8518 (tp30) cc_final: 0.8100 (tm-30) REVERT: aB 302 LYS cc_start: 0.9171 (tmtt) cc_final: 0.8553 (ttmm) REVERT: aB 305 PHE cc_start: 0.8899 (t80) cc_final: 0.8673 (t80) REVERT: bB 352 LYS cc_start: 0.8991 (tmtt) cc_final: 0.8511 (pptt) REVERT: cB 402 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8767 (ttmm) outliers start: 110 outliers final: 54 residues processed: 341 average time/residue: 0.1813 time to fit residues: 73.8537 Evaluate side-chains 407 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 313 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain SA residue 304 GLU Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 303 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain OB residue 455 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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 = 0.3393 r_free = 0.3393 target = 0.079217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.071656 restraints weight = 23694.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073491 restraints weight = 9074.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.074660 restraints weight = 4603.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075469 restraints weight = 2737.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076022 restraints weight = 1830.474| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.6493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.159 8700 Z= 2.313 Angle : 2.731 18.308 11300 Z= 1.311 Chirality : 0.137 0.337 800 Planarity : 0.011 0.039 1500 Dihedral : 26.653 89.592 1021 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 118.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.75 % Favored : 76.25 % Rotamer: Outliers : 19.33 % Allowed : 31.50 % Favored : 49.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.15 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.091 0.011 PHEaA 203 Details of bonding type rmsd covalent geometry : bond 0.05108 ( 8700) covalent geometry : angle 2.73095 (11300) hydrogen bonds : bond 0.12416 ( 139) hydrogen bonds : angle 8.61887 ( 381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 319 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8386 (mp0) REVERT: A 6 LYS cc_start: 0.9087 (tttt) cc_final: 0.8656 (tttm) REVERT: A 7 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8154 (m-10) REVERT: K 104 GLU cc_start: 0.8624 (mp0) cc_final: 0.8399 (mp0) REVERT: K 107 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8502 (m-80) REVERT: L 207 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8907 (m-80) REVERT: M 306 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8618 (tttt) REVERT: M 307 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: B 4 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8459 (mp0) REVERT: C 4 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: C 6 LYS cc_start: 0.9118 (tttt) cc_final: 0.8888 (ttmt) REVERT: Y 106 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8842 (ttmt) REVERT: m 304 GLU cc_start: 0.8669 (mp0) cc_final: 0.8405 (mp0) REVERT: E 4 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: E 6 LYS cc_start: 0.9030 (tttt) cc_final: 0.8762 (tttp) REVERT: r 104 GLU cc_start: 0.8649 (mp0) cc_final: 0.8362 (mp0) REVERT: u 404 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8091 (mm-30) REVERT: u 406 LYS cc_start: 0.8996 (mptt) cc_final: 0.8597 (ttmt) REVERT: F 7 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.8309 (m-10) REVERT: y 107 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: z 206 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8857 (ttpt) REVERT: z 207 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8247 (m-10) REVERT: 0 307 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: G 7 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.7848 (m-10) REVERT: 6 206 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8806 (ttpt) REVERT: 6 207 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: H 4 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: H 6 LYS cc_start: 0.9338 (tttt) cc_final: 0.8908 (ttmt) REVERT: I 6 LYS cc_start: 0.9028 (tttt) cc_final: 0.8746 (tttm) REVERT: JA 104 GLU cc_start: 0.4561 (OUTLIER) cc_final: 0.3695 (pm20) REVERT: J 4 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7830 (tm-30) REVERT: RA 204 GLU cc_start: 0.9001 (pm20) cc_final: 0.8658 (pm20) REVERT: TA 404 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7904 (tm-30) REVERT: a 3 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.7580 (t80) REVERT: a 4 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: XA 52 LYS cc_start: 0.9099 (tmtt) cc_final: 0.8872 (tmtt) REVERT: XA 55 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7871 (t80) REVERT: XA 56 LYS cc_start: 0.9266 (tmtt) cc_final: 0.8926 (tttp) REVERT: YA 104 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: ZA 152 LYS cc_start: 0.9063 (tmtt) cc_final: 0.8862 (tmtt) REVERT: ZA 155 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.7945 (t80) REVERT: ZA 156 LYS cc_start: 0.9410 (tmtt) cc_final: 0.9162 (tttm) REVERT: aA 203 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8301 (t80) REVERT: bA 255 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7884 (t80) REVERT: cA 302 LYS cc_start: 0.9223 (tmtt) cc_final: 0.9015 (tmtt) REVERT: cA 303 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.6891 (t80) REVERT: cA 304 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8026 (tp30) REVERT: dA 355 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7644 (t80) REVERT: eA 403 PHE cc_start: 0.9172 (OUTLIER) cc_final: 0.7186 (t80) REVERT: fA 452 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8913 (tmtt) REVERT: fA 455 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.8010 (t80) REVERT: fA 456 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9121 (tttm) REVERT: mA 55 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.6968 (t80) REVERT: mA 56 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9113 (tttp) REVERT: oA 156 LYS cc_start: 0.9348 (tmtt) cc_final: 0.9092 (tttp) REVERT: qA 256 LYS cc_start: 0.9231 (tmtt) cc_final: 0.8875 (tmtt) REVERT: rA 304 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: rA 305 PHE cc_start: 0.8928 (t80) cc_final: 0.8480 (t80) REVERT: sA 355 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.6902 (t80) REVERT: uA 455 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.6862 (t80) REVERT: uA 456 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.9081 (tttp) REVERT: 1A 56 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9019 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: 4A 205 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8032 (t80) REVERT: 4A 206 LYS cc_start: 0.9205 (tttm) cc_final: 0.8860 (tttm) REVERT: 5A 256 LYS cc_start: 0.9192 (tmtt) cc_final: 0.8809 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9092 (tttm) REVERT: d 5 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8373 (t80) REVERT: GB 56 LYS cc_start: 0.9356 (tmtt) cc_final: 0.9094 (tmtt) REVERT: HB 105 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8340 (t80) REVERT: JB 204 GLU cc_start: 0.8632 (tp30) cc_final: 0.8148 (pm20) REVERT: LB 302 LYS cc_start: 0.9167 (tmtt) cc_final: 0.8846 (ttmm) REVERT: LB 305 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8240 (t80) REVERT: LB 306 LYS cc_start: 0.9370 (tttm) cc_final: 0.9047 (tttm) REVERT: OB 456 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9124 (tttm) REVERT: XB 152 LYS cc_start: 0.8964 (tmtt) cc_final: 0.8518 (pptt) REVERT: XB 155 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7752 (t80) REVERT: XB 157 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7500 (t80) REVERT: YB 205 PHE cc_start: 0.8954 (t80) cc_final: 0.8680 (t80) REVERT: ZB 252 LYS cc_start: 0.9140 (tmtt) cc_final: 0.8447 (pptt) REVERT: ZB 256 LYS cc_start: 0.9325 (tmtt) cc_final: 0.9093 (tttp) REVERT: bB 352 LYS cc_start: 0.9081 (tmtt) cc_final: 0.8493 (pptt) REVERT: cB 402 LYS cc_start: 0.9143 (tmtt) cc_final: 0.8740 (ttmm) REVERT: dB 452 LYS cc_start: 0.9072 (tmtt) cc_final: 0.8433 (pptt) outliers start: 116 outliers final: 57 residues processed: 349 average time/residue: 0.1691 time to fit residues: 71.0459 Evaluate side-chains 421 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 318 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain OB residue 456 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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 = 0.3399 r_free = 0.3399 target = 0.079676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072044 restraints weight = 23498.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073867 restraints weight = 8943.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075042 restraints weight = 4552.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075840 restraints weight = 2709.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076426 restraints weight = 1812.767| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.170 8700 Z= 2.311 Angle : 2.729 19.337 11300 Z= 1.311 Chirality : 0.137 0.340 800 Planarity : 0.011 0.040 1500 Dihedral : 26.554 89.790 1021 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 117.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.25 % Favored : 75.75 % Rotamer: Outliers : 21.33 % Allowed : 30.17 % Favored : 48.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.091 0.011 PHEaA 203 Details of bonding type rmsd covalent geometry : bond 0.05104 ( 8700) covalent geometry : angle 2.72923 (11300) hydrogen bonds : bond 0.12246 ( 139) hydrogen bonds : angle 8.70116 ( 381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 318 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: A 6 LYS cc_start: 0.9069 (tttt) cc_final: 0.8724 (tttm) REVERT: A 7 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: K 104 GLU cc_start: 0.8631 (mp0) cc_final: 0.8380 (mp0) REVERT: K 107 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: L 207 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9002 (m-80) REVERT: M 306 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8638 (tttt) REVERT: M 307 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.8088 (m-10) REVERT: B 4 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: C 4 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: C 6 LYS cc_start: 0.9147 (tttt) cc_final: 0.8912 (ttmt) REVERT: Y 106 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8842 (ttmt) REVERT: D 4 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7897 (tm-30) REVERT: k 104 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: E 4 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: E 6 LYS cc_start: 0.9032 (tttt) cc_final: 0.8752 (tttp) REVERT: r 104 GLU cc_start: 0.8685 (mp0) cc_final: 0.8396 (mp0) REVERT: u 404 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8036 (mm-30) REVERT: u 406 LYS cc_start: 0.8968 (mptt) cc_final: 0.8517 (ttmt) REVERT: F 7 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: y 107 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: z 206 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8853 (ttpt) REVERT: z 207 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.8222 (m-10) REVERT: 0 307 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8606 (m-80) REVERT: G 7 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.7811 (m-10) REVERT: 6 206 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8838 (ttpt) REVERT: 6 207 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8114 (m-10) REVERT: H 4 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7853 (tm-30) REVERT: H 6 LYS cc_start: 0.9343 (tttt) cc_final: 0.8905 (ttmt) REVERT: JA 104 GLU cc_start: 0.4581 (OUTLIER) cc_final: 0.3717 (pm20) REVERT: J 4 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: RA 204 GLU cc_start: 0.9001 (pm20) cc_final: 0.8633 (pm20) REVERT: TA 404 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7985 (tm-30) REVERT: a 3 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.7620 (t80) REVERT: a 4 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7978 (tp30) REVERT: XA 52 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8801 (tmtt) REVERT: XA 55 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7821 (t80) REVERT: XA 56 LYS cc_start: 0.9270 (tmtt) cc_final: 0.8939 (tttp) REVERT: YA 103 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8144 (t80) REVERT: YA 104 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8073 (tp30) REVERT: ZA 155 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8019 (t80) REVERT: ZA 156 LYS cc_start: 0.9396 (tmtt) cc_final: 0.9142 (tttm) REVERT: aA 203 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8351 (t80) REVERT: cA 302 LYS cc_start: 0.9267 (tmtt) cc_final: 0.9056 (tttm) REVERT: cA 303 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.7104 (t80) REVERT: cA 304 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: dA 355 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7644 (t80) REVERT: eA 403 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8439 (t80) REVERT: eA 404 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7898 (tm-30) REVERT: fA 455 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.8107 (t80) REVERT: fA 456 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9123 (tttm) REVERT: mA 55 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.6971 (t80) REVERT: mA 56 LYS cc_start: 0.9351 (tmtt) cc_final: 0.9086 (tttp) REVERT: oA 152 LYS cc_start: 0.8979 (tmtt) cc_final: 0.8733 (tmtt) REVERT: oA 156 LYS cc_start: 0.9350 (tmtt) cc_final: 0.9095 (tttp) REVERT: qA 256 LYS cc_start: 0.9221 (tmtt) cc_final: 0.8700 (tmtt) REVERT: rA 304 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8110 (tp30) REVERT: rA 305 PHE cc_start: 0.8928 (t80) cc_final: 0.8649 (t80) REVERT: sA 355 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7031 (t80) REVERT: sA 356 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8654 (tmtt) REVERT: uA 456 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9146 (tttp) REVERT: 1A 56 LYS cc_start: 0.9374 (tmtt) cc_final: 0.9006 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8477 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9366 (tmtt) cc_final: 0.9053 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8166 (t80) REVERT: 4A 206 LYS cc_start: 0.9210 (tttm) cc_final: 0.8777 (tttm) REVERT: 7A 356 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9071 (tttm) REVERT: d 5 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8320 (t80) REVERT: HB 105 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.8279 (t80) REVERT: JB 204 GLU cc_start: 0.8683 (tp30) cc_final: 0.8131 (pm20) REVERT: KB 256 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8818 (tmtt) REVERT: LB 302 LYS cc_start: 0.9201 (tmtt) cc_final: 0.8897 (ttmm) REVERT: LB 306 LYS cc_start: 0.9376 (tttm) cc_final: 0.9142 (tttm) REVERT: OB 456 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9119 (tttm) REVERT: VB 52 LYS cc_start: 0.9049 (tmtt) cc_final: 0.8476 (pptt) REVERT: XB 152 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8528 (pptt) REVERT: XB 157 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7702 (t80) REVERT: YB 205 PHE cc_start: 0.8985 (t80) cc_final: 0.8626 (t80) REVERT: ZB 252 LYS cc_start: 0.9061 (tmtt) cc_final: 0.8438 (pptt) REVERT: aB 304 GLU cc_start: 0.8620 (tp30) cc_final: 0.8111 (tm-30) REVERT: bB 352 LYS cc_start: 0.9083 (tmtt) cc_final: 0.8527 (pptt) REVERT: cB 402 LYS cc_start: 0.9164 (tmtt) cc_final: 0.8727 (ttmm) REVERT: dB 452 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8447 (pptt) outliers start: 128 outliers final: 67 residues processed: 355 average time/residue: 0.1704 time to fit residues: 72.5918 Evaluate side-chains 429 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 318 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain OB residue 456 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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 = 0.3407 r_free = 0.3407 target = 0.079857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072247 restraints weight = 23405.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.074078 restraints weight = 8996.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.075248 restraints weight = 4616.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076047 restraints weight = 2765.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076613 restraints weight = 1849.952| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.156 8700 Z= 2.309 Angle : 2.726 19.922 11300 Z= 1.309 Chirality : 0.138 0.344 800 Planarity : 0.011 0.041 1500 Dihedral : 26.366 89.908 1021 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 116.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.50 % Favored : 74.50 % Rotamer: Outliers : 21.50 % Allowed : 29.83 % Favored : 48.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.19 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.095 0.011 PHEaA 203 Details of bonding type rmsd covalent geometry : bond 0.05102 ( 8700) covalent geometry : angle 2.72623 (11300) hydrogen bonds : bond 0.12266 ( 139) hydrogen bonds : angle 8.71753 ( 381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 318 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: A 6 LYS cc_start: 0.9063 (tttt) cc_final: 0.8726 (tttm) REVERT: A 7 PHE cc_start: 0.9440 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: K 104 GLU cc_start: 0.8636 (mp0) cc_final: 0.8376 (mp0) REVERT: K 107 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: L 207 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8970 (m-80) REVERT: M 304 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8199 (mp0) REVERT: M 306 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8653 (tttt) REVERT: M 307 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.8007 (m-10) REVERT: B 4 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: C 4 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8533 (mp0) REVERT: C 6 LYS cc_start: 0.9166 (tttt) cc_final: 0.8785 (tttm) REVERT: Y 106 LYS cc_start: 0.9145 (mtpt) cc_final: 0.8866 (ttmt) REVERT: D 4 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: k 104 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: E 4 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8220 (mp0) REVERT: E 6 LYS cc_start: 0.9012 (tttt) cc_final: 0.8735 (tttp) REVERT: r 104 GLU cc_start: 0.8675 (mp0) cc_final: 0.8397 (mp0) REVERT: u 406 LYS cc_start: 0.8958 (mptt) cc_final: 0.8568 (ttmt) REVERT: F 7 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8322 (m-10) REVERT: y 104 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: y 107 PHE cc_start: 0.9375 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: z 206 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8852 (ttpt) REVERT: z 207 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.8228 (m-10) REVERT: 0 307 PHE cc_start: 0.9444 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: G 7 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: 6 206 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8845 (ttpt) REVERT: 6 207 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8123 (m-10) REVERT: H 4 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: H 6 LYS cc_start: 0.9323 (tttt) cc_final: 0.8883 (ttmt) REVERT: JA 104 GLU cc_start: 0.4653 (OUTLIER) cc_final: 0.3795 (pm20) REVERT: J 4 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: QA 104 GLU cc_start: 0.8935 (pm20) cc_final: 0.7645 (mm-30) REVERT: RA 204 GLU cc_start: 0.9013 (pm20) cc_final: 0.8639 (pm20) REVERT: TA 404 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8016 (tm-30) REVERT: a 3 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.7607 (t80) REVERT: a 4 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: XA 52 LYS cc_start: 0.9031 (tmtt) cc_final: 0.8766 (tmtt) REVERT: XA 55 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7820 (t80) REVERT: XA 56 LYS cc_start: 0.9271 (tmtt) cc_final: 0.8946 (tttp) REVERT: YA 103 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8130 (t80) REVERT: YA 104 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: ZA 155 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7977 (t80) REVERT: ZA 156 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9157 (tttm) REVERT: aA 203 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8175 (t80) REVERT: bA 255 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7797 (t80) REVERT: cA 303 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.7203 (t80) REVERT: cA 304 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8224 (tm-30) REVERT: dA 355 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7655 (t80) REVERT: eA 403 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8450 (t80) REVERT: eA 404 GLU cc_start: 0.8597 (tm-30) cc_final: 0.7989 (tm-30) REVERT: fA 455 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8035 (t80) REVERT: fA 456 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9125 (tttp) REVERT: mA 55 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.6982 (t80) REVERT: mA 56 LYS cc_start: 0.9344 (tmtt) cc_final: 0.9077 (tttp) REVERT: oA 156 LYS cc_start: 0.9355 (tmtt) cc_final: 0.9087 (tttp) REVERT: qA 256 LYS cc_start: 0.9226 (tmtt) cc_final: 0.8991 (tttm) REVERT: rA 304 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: rA 305 PHE cc_start: 0.8925 (t80) cc_final: 0.8580 (t80) REVERT: sA 355 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7126 (t80) REVERT: uA 456 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9143 (tttp) REVERT: 1A 56 LYS cc_start: 0.9392 (tmtt) cc_final: 0.9054 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9357 (tmtt) cc_final: 0.8980 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8104 (t80) REVERT: 4A 206 LYS cc_start: 0.9216 (tttm) cc_final: 0.8860 (tttm) REVERT: 5A 256 LYS cc_start: 0.9243 (tmtt) cc_final: 0.8905 (tmtt) REVERT: 6A 302 LYS cc_start: 0.9168 (tmtt) cc_final: 0.8929 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9066 (tttm) REVERT: 9A 456 LYS cc_start: 0.9180 (tttm) cc_final: 0.8855 (tmtt) REVERT: d 5 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8370 (t80) REVERT: HB 105 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8337 (t80) REVERT: JB 204 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: KB 256 LYS cc_start: 0.9167 (tmtt) cc_final: 0.8839 (tmtt) REVERT: LB 302 LYS cc_start: 0.9197 (tmtt) cc_final: 0.8897 (ttmm) REVERT: LB 306 LYS cc_start: 0.9375 (tttm) cc_final: 0.9140 (tttm) REVERT: MB 356 LYS cc_start: 0.9104 (tmtt) cc_final: 0.8887 (tmtt) REVERT: OB 456 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9133 (tttm) REVERT: VB 52 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8438 (pptt) REVERT: XB 152 LYS cc_start: 0.8995 (tmtt) cc_final: 0.8527 (pptt) REVERT: XB 157 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7681 (t80) REVERT: ZB 252 LYS cc_start: 0.9150 (tmtt) cc_final: 0.8532 (pptt) REVERT: aB 304 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: bB 352 LYS cc_start: 0.9083 (tmtt) cc_final: 0.8552 (pptt) REVERT: dB 452 LYS cc_start: 0.9122 (tmtt) cc_final: 0.8458 (pptt) outliers start: 129 outliers final: 66 residues processed: 353 average time/residue: 0.1710 time to fit residues: 72.6194 Evaluate side-chains 433 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 316 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 204 GLU Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain OB residue 456 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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 = 0.3414 r_free = 0.3414 target = 0.080109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072386 restraints weight = 23448.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.074249 restraints weight = 9040.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075434 restraints weight = 4626.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076237 restraints weight = 2762.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076854 restraints weight = 1849.908| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.152 8700 Z= 2.310 Angle : 2.730 20.301 11300 Z= 1.311 Chirality : 0.138 0.345 800 Planarity : 0.011 0.041 1500 Dihedral : 26.279 89.944 1021 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 116.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.25 % Favored : 74.75 % Rotamer: Outliers : 21.50 % Allowed : 31.17 % Favored : 47.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.14 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.095 0.011 PHEaA 203 Details of bonding type rmsd covalent geometry : bond 0.05103 ( 8700) covalent geometry : angle 2.72980 (11300) hydrogen bonds : bond 0.12269 ( 139) hydrogen bonds : angle 8.79842 ( 381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 318 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: A 6 LYS cc_start: 0.9067 (tttt) cc_final: 0.8710 (tttm) REVERT: A 7 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: K 104 GLU cc_start: 0.8637 (mp0) cc_final: 0.8367 (mp0) REVERT: K 107 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: L 207 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8947 (m-80) REVERT: M 304 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: M 306 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8685 (tttt) REVERT: M 307 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.8007 (m-10) REVERT: B 4 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8470 (mp0) REVERT: C 4 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: C 6 LYS cc_start: 0.9171 (tttt) cc_final: 0.8794 (tttp) REVERT: Y 106 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8869 (ttmt) REVERT: D 4 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: k 104 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: E 4 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: E 6 LYS cc_start: 0.9006 (tttt) cc_final: 0.8727 (tttp) REVERT: r 104 GLU cc_start: 0.8684 (mp0) cc_final: 0.8395 (mp0) REVERT: u 404 GLU cc_start: 0.8789 (mp0) cc_final: 0.8324 (mp0) REVERT: u 406 LYS cc_start: 0.9034 (mptt) cc_final: 0.8634 (ttmt) REVERT: F 7 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: y 104 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: y 107 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: z 206 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8863 (ttpt) REVERT: z 207 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8210 (m-10) REVERT: 0 307 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: G 7 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.7814 (m-10) REVERT: 6 206 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8849 (ttpt) REVERT: 6 207 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8116 (m-10) REVERT: H 4 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7863 (tm-30) REVERT: H 6 LYS cc_start: 0.9323 (tttt) cc_final: 0.8878 (ttmt) REVERT: JA 104 GLU cc_start: 0.4574 (OUTLIER) cc_final: 0.3720 (pm20) REVERT: J 4 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7928 (tm-30) REVERT: QA 104 GLU cc_start: 0.8920 (pm20) cc_final: 0.7636 (mm-30) REVERT: RA 204 GLU cc_start: 0.9014 (pm20) cc_final: 0.8623 (pm20) REVERT: TA 404 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8006 (tm-30) REVERT: a 3 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8500 (t80) REVERT: a 4 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: XA 52 LYS cc_start: 0.9031 (tmtt) cc_final: 0.8754 (tmtt) REVERT: XA 55 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7842 (t80) REVERT: XA 56 LYS cc_start: 0.9273 (tmtt) cc_final: 0.8945 (tttp) REVERT: YA 103 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8127 (t80) REVERT: YA 104 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: ZA 155 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8043 (t80) REVERT: ZA 156 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9118 (tttp) REVERT: aA 203 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8228 (t80) REVERT: bA 255 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7865 (t80) REVERT: cA 304 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8166 (tp30) REVERT: dA 355 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7671 (t80) REVERT: eA 403 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8535 (t80) REVERT: eA 404 GLU cc_start: 0.8576 (tm-30) cc_final: 0.7990 (tm-30) REVERT: fA 455 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8085 (t80) REVERT: fA 456 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9123 (tttm) REVERT: mA 56 LYS cc_start: 0.9318 (tmtt) cc_final: 0.9068 (tttp) REVERT: oA 156 LYS cc_start: 0.9357 (tmtt) cc_final: 0.9088 (tttp) REVERT: qA 252 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8833 (tmtt) REVERT: qA 256 LYS cc_start: 0.9213 (tmtt) cc_final: 0.8972 (tttm) REVERT: rA 304 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: rA 305 PHE cc_start: 0.8928 (t80) cc_final: 0.8574 (t80) REVERT: sA 355 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7225 (t80) REVERT: uA 456 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9123 (tttp) REVERT: 1A 56 LYS cc_start: 0.9407 (tmtt) cc_final: 0.9082 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8527 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9355 (tmtt) cc_final: 0.8980 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8202 (t80) REVERT: 4A 206 LYS cc_start: 0.9214 (tttm) cc_final: 0.8794 (tttm) REVERT: 5A 256 LYS cc_start: 0.9236 (tmtt) cc_final: 0.8835 (tmtt) REVERT: 6A 302 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8925 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9026 (tttm) REVERT: 9A 456 LYS cc_start: 0.9182 (tttm) cc_final: 0.8672 (tmtt) REVERT: d 5 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8434 (t80) REVERT: GB 56 LYS cc_start: 0.9355 (tmtt) cc_final: 0.9074 (tmtt) REVERT: HB 105 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8344 (t80) REVERT: JB 205 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8307 (t80) REVERT: KB 256 LYS cc_start: 0.9167 (tmtt) cc_final: 0.8854 (tmtt) REVERT: LB 302 LYS cc_start: 0.9204 (tmtt) cc_final: 0.8896 (ttmm) REVERT: LB 306 LYS cc_start: 0.9373 (tttm) cc_final: 0.9135 (tttm) REVERT: VB 52 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8441 (pptt) REVERT: XB 152 LYS cc_start: 0.9044 (tmtt) cc_final: 0.8518 (pptt) REVERT: XB 157 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7662 (t80) REVERT: ZB 252 LYS cc_start: 0.9158 (tmtt) cc_final: 0.8532 (pptt) REVERT: aB 304 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: bB 352 LYS cc_start: 0.9078 (tmtt) cc_final: 0.8431 (pptt) REVERT: dB 452 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8442 (pptt) outliers start: 129 outliers final: 71 residues processed: 353 average time/residue: 0.1804 time to fit residues: 76.5713 Evaluate side-chains 437 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 318 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain U residue 406 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain SA residue 304 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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 = 0.3411 r_free = 0.3411 target = 0.079976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072262 restraints weight = 23351.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074126 restraints weight = 9120.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075329 restraints weight = 4652.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076144 restraints weight = 2763.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.076723 restraints weight = 1839.831| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.152 8700 Z= 2.309 Angle : 2.727 20.319 11300 Z= 1.309 Chirality : 0.138 0.352 800 Planarity : 0.011 0.042 1500 Dihedral : 26.234 89.765 1021 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 118.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.50 % Favored : 74.50 % Rotamer: Outliers : 22.00 % Allowed : 30.33 % Favored : 47.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.09 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.097 0.011 PHEaA 203 Details of bonding type rmsd covalent geometry : bond 0.05102 ( 8700) covalent geometry : angle 2.72659 (11300) hydrogen bonds : bond 0.12179 ( 139) hydrogen bonds : angle 8.86127 ( 381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 319 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: A 6 LYS cc_start: 0.9069 (tttt) cc_final: 0.8723 (tttm) REVERT: A 7 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: K 104 GLU cc_start: 0.8635 (mp0) cc_final: 0.8355 (mp0) REVERT: K 107 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: L 207 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.8941 (m-80) REVERT: M 304 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: M 306 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8691 (tttt) REVERT: M 307 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: B 4 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8467 (mp0) REVERT: C 4 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8538 (mp0) REVERT: C 6 LYS cc_start: 0.9176 (tttt) cc_final: 0.8812 (tttm) REVERT: Y 106 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8869 (ttmt) REVERT: k 104 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: E 4 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: E 6 LYS cc_start: 0.8998 (tttt) cc_final: 0.8723 (tttp) REVERT: r 104 GLU cc_start: 0.8690 (mp0) cc_final: 0.8399 (mp0) REVERT: u 404 GLU cc_start: 0.8867 (mp0) cc_final: 0.8378 (mp0) REVERT: u 406 LYS cc_start: 0.9041 (mptt) cc_final: 0.8654 (ttmt) REVERT: F 7 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.8293 (m-10) REVERT: y 107 PHE cc_start: 0.9363 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: z 206 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8862 (ttpt) REVERT: z 207 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: 0 307 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8610 (m-80) REVERT: G 7 PHE cc_start: 0.9293 (OUTLIER) cc_final: 0.7801 (m-10) REVERT: 6 206 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8852 (ttpt) REVERT: 6 207 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: H 4 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: H 6 LYS cc_start: 0.9321 (tttt) cc_final: 0.8878 (ttmt) REVERT: EA 302 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8810 (ttmm) REVERT: JA 104 GLU cc_start: 0.4588 (OUTLIER) cc_final: 0.3729 (pm20) REVERT: J 4 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: QA 104 GLU cc_start: 0.8928 (pm20) cc_final: 0.7649 (mm-30) REVERT: RA 204 GLU cc_start: 0.9015 (pm20) cc_final: 0.8614 (pm20) REVERT: TA 404 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8007 (tm-30) REVERT: a 3 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8493 (t80) REVERT: a 4 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8015 (tp30) REVERT: XA 52 LYS cc_start: 0.9031 (tmtt) cc_final: 0.8751 (tmtt) REVERT: XA 55 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7851 (t80) REVERT: XA 56 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8946 (tttp) REVERT: YA 103 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8115 (t80) REVERT: YA 104 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: ZA 155 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8087 (t80) REVERT: ZA 156 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9140 (tttp) REVERT: aA 203 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8251 (t80) REVERT: bA 255 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7886 (t80) REVERT: cA 304 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8114 (tp30) REVERT: dA 355 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7631 (t80) REVERT: eA 403 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8540 (t80) REVERT: eA 404 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8055 (tm-30) REVERT: fA 455 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8112 (t80) REVERT: fA 456 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9125 (tttm) REVERT: mA 56 LYS cc_start: 0.9319 (tmtt) cc_final: 0.9069 (tttp) REVERT: oA 156 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9103 (tttp) REVERT: qA 252 LYS cc_start: 0.9081 (tmtt) cc_final: 0.8866 (tmtt) REVERT: qA 256 LYS cc_start: 0.9209 (tmtt) cc_final: 0.8966 (tttm) REVERT: rA 304 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: rA 305 PHE cc_start: 0.8969 (t80) cc_final: 0.8643 (t80) REVERT: sA 355 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7126 (t80) REVERT: uA 456 LYS cc_start: 0.9369 (OUTLIER) cc_final: 0.9127 (tttp) REVERT: 1A 56 LYS cc_start: 0.9386 (tmtt) cc_final: 0.9086 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8507 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9352 (tmtt) cc_final: 0.8959 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8205 (t80) REVERT: 4A 206 LYS cc_start: 0.9219 (tttm) cc_final: 0.8798 (tttm) REVERT: 6A 302 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8911 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9019 (tttm) REVERT: 9A 456 LYS cc_start: 0.9155 (tttm) cc_final: 0.8624 (tmtt) REVERT: d 5 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8405 (t80) REVERT: GB 56 LYS cc_start: 0.9347 (tmtt) cc_final: 0.9036 (tmtt) REVERT: HB 105 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8349 (t80) REVERT: JB 205 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.7848 (t80) REVERT: LB 302 LYS cc_start: 0.9207 (tmtt) cc_final: 0.8892 (ttmm) REVERT: LB 306 LYS cc_start: 0.9370 (tttm) cc_final: 0.9127 (tttm) REVERT: VB 52 LYS cc_start: 0.9005 (tmtt) cc_final: 0.8452 (pptt) REVERT: XB 152 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8515 (pptt) REVERT: XB 157 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7633 (t80) REVERT: YB 205 PHE cc_start: 0.9058 (t80) cc_final: 0.8809 (t80) REVERT: ZB 252 LYS cc_start: 0.9128 (tmtt) cc_final: 0.8467 (pptt) REVERT: aB 304 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: bB 352 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8429 (pptt) REVERT: dB 452 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8418 (pptt) outliers start: 132 outliers final: 72 residues processed: 356 average time/residue: 0.1850 time to fit residues: 79.0360 Evaluate side-chains 440 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 320 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain U residue 406 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 302 LYS Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain SA residue 304 GLU Chi-restraints excluded: chain TA residue 406 LYS Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 402 LYS Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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 = 0.3411 r_free = 0.3411 target = 0.079943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072352 restraints weight = 23466.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.074185 restraints weight = 9041.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075377 restraints weight = 4595.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076170 restraints weight = 2722.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076756 restraints weight = 1809.414| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.152 8700 Z= 2.309 Angle : 2.728 20.461 11300 Z= 1.311 Chirality : 0.138 0.370 800 Planarity : 0.011 0.041 1500 Dihedral : 26.183 89.662 1021 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 118.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.50 % Favored : 74.50 % Rotamer: Outliers : 22.00 % Allowed : 30.17 % Favored : 47.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.05 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.095 0.011 PHEaA 203 Details of bonding type rmsd covalent geometry : bond 0.05102 ( 8700) covalent geometry : angle 2.72824 (11300) hydrogen bonds : bond 0.12166 ( 139) hydrogen bonds : angle 8.85528 ( 381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 320 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: A 6 LYS cc_start: 0.9072 (tttt) cc_final: 0.8710 (tttm) REVERT: A 7 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.8361 (m-80) REVERT: K 104 GLU cc_start: 0.8636 (mp0) cc_final: 0.8355 (mp0) REVERT: K 107 PHE cc_start: 0.9396 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: L 207 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8971 (m-80) REVERT: M 304 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: M 306 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8695 (tttt) REVERT: M 307 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8004 (m-10) REVERT: B 4 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8460 (mp0) REVERT: C 4 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: C 6 LYS cc_start: 0.9178 (tttt) cc_final: 0.8813 (tttm) REVERT: Y 106 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8873 (ttmt) REVERT: k 104 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8297 (mp0) REVERT: E 4 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: E 6 LYS cc_start: 0.8992 (tttt) cc_final: 0.8716 (tttp) REVERT: r 104 GLU cc_start: 0.8699 (mp0) cc_final: 0.8415 (mp0) REVERT: u 404 GLU cc_start: 0.8871 (mp0) cc_final: 0.8395 (mp0) REVERT: u 406 LYS cc_start: 0.9043 (mptt) cc_final: 0.8650 (ttmt) REVERT: F 7 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: y 104 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: y 107 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8383 (m-80) REVERT: z 206 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8846 (ttpt) REVERT: z 207 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: 0 307 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.8670 (m-80) REVERT: G 6 LYS cc_start: 0.9364 (tttt) cc_final: 0.8817 (tttm) REVERT: G 7 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.7873 (m-10) REVERT: 6 206 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8854 (ttpt) REVERT: 6 207 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: H 4 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: H 6 LYS cc_start: 0.9312 (tttt) cc_final: 0.8854 (tttp) REVERT: EA 302 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8805 (ttmm) REVERT: JA 104 GLU cc_start: 0.4587 (OUTLIER) cc_final: 0.3730 (pm20) REVERT: J 4 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: QA 104 GLU cc_start: 0.8930 (pm20) cc_final: 0.7634 (mm-30) REVERT: RA 204 GLU cc_start: 0.9014 (pm20) cc_final: 0.8607 (pm20) REVERT: TA 404 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8002 (tm-30) REVERT: a 3 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8492 (t80) REVERT: a 4 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: XA 52 LYS cc_start: 0.9032 (tmtt) cc_final: 0.8749 (tmtt) REVERT: XA 55 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7841 (t80) REVERT: XA 56 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8960 (tttp) REVERT: YA 103 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8117 (t80) REVERT: YA 104 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: ZA 155 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8088 (t80) REVERT: ZA 156 LYS cc_start: 0.9415 (tmtt) cc_final: 0.9142 (tttp) REVERT: aA 203 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8205 (t80) REVERT: bA 255 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7878 (t80) REVERT: cA 304 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: dA 355 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7672 (t80) REVERT: eA 403 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8527 (t80) REVERT: eA 404 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8074 (tm-30) REVERT: fA 455 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8134 (t80) REVERT: fA 456 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9125 (tttm) REVERT: mA 56 LYS cc_start: 0.9319 (tttt) cc_final: 0.9073 (tttp) REVERT: oA 156 LYS cc_start: 0.9368 (tmtt) cc_final: 0.9101 (tttp) REVERT: qA 252 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8857 (tmtt) REVERT: rA 304 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: rA 305 PHE cc_start: 0.8953 (t80) cc_final: 0.8623 (t80) REVERT: sA 355 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7218 (t80) REVERT: uA 456 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9119 (tttp) REVERT: 1A 56 LYS cc_start: 0.9395 (tmtt) cc_final: 0.9064 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8504 (tm-30) REVERT: 4A 205 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8207 (t80) REVERT: 4A 206 LYS cc_start: 0.9219 (tttm) cc_final: 0.8773 (tttm) REVERT: 5A 256 LYS cc_start: 0.9250 (tmtt) cc_final: 0.8867 (tmtt) REVERT: 6A 302 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8903 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9034 (tttm) REVERT: 9A 456 LYS cc_start: 0.9154 (tttm) cc_final: 0.8618 (tmtt) REVERT: d 5 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8410 (t80) REVERT: GB 56 LYS cc_start: 0.9351 (tmtt) cc_final: 0.9049 (tmtt) REVERT: HB 105 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.8347 (t80) REVERT: JB 205 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8015 (t80) REVERT: KB 256 LYS cc_start: 0.9156 (tmtt) cc_final: 0.8862 (tmtt) REVERT: LB 302 LYS cc_start: 0.9205 (tmtt) cc_final: 0.8892 (ttmm) REVERT: LB 306 LYS cc_start: 0.9362 (tttm) cc_final: 0.9124 (tttm) REVERT: MB 356 LYS cc_start: 0.9095 (tmtt) cc_final: 0.8888 (tmtt) REVERT: VB 52 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8452 (pptt) REVERT: VB 56 LYS cc_start: 0.9443 (tmtt) cc_final: 0.9142 (tptp) REVERT: XB 152 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8511 (pptt) REVERT: XB 157 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7628 (t80) REVERT: YB 205 PHE cc_start: 0.9056 (t80) cc_final: 0.8808 (t80) REVERT: ZB 252 LYS cc_start: 0.9145 (tmtt) cc_final: 0.8489 (pptt) REVERT: aB 304 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: bB 352 LYS cc_start: 0.9131 (tmtt) cc_final: 0.8421 (pptt) REVERT: dB 452 LYS cc_start: 0.9094 (tmtt) cc_final: 0.8347 (pptt) outliers start: 132 outliers final: 76 residues processed: 357 average time/residue: 0.1854 time to fit residues: 79.3269 Evaluate side-chains 445 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 320 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 406 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 302 LYS Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain SA residue 304 GLU Chi-restraints excluded: chain TA residue 406 LYS Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 302 LYS Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 402 LYS Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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 = 0.3399 r_free = 0.3399 target = 0.079235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.072006 restraints weight = 23500.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.073773 restraints weight = 8975.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.074905 restraints weight = 4539.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075681 restraints weight = 2674.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.076223 restraints weight = 1772.803| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.152 8700 Z= 2.309 Angle : 2.729 20.642 11300 Z= 1.311 Chirality : 0.138 0.383 800 Planarity : 0.011 0.043 1500 Dihedral : 26.140 89.632 1021 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 118.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.00 % Favored : 74.00 % Rotamer: Outliers : 21.83 % Allowed : 30.17 % Favored : 48.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.05 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.100 0.011 PHEcA 303 Details of bonding type rmsd covalent geometry : bond 0.05100 ( 8700) covalent geometry : angle 2.72939 (11300) hydrogen bonds : bond 0.12133 ( 139) hydrogen bonds : angle 8.84439 ( 381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 320 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: A 6 LYS cc_start: 0.9069 (tttt) cc_final: 0.8715 (tttm) REVERT: A 7 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: K 104 GLU cc_start: 0.8637 (mp0) cc_final: 0.8362 (mp0) REVERT: K 107 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: L 207 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8979 (m-80) REVERT: M 304 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: M 306 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8695 (tttt) REVERT: M 307 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.8016 (m-10) REVERT: B 4 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: C 4 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8535 (mp0) REVERT: C 6 LYS cc_start: 0.9176 (tttt) cc_final: 0.8816 (tttm) REVERT: Y 106 LYS cc_start: 0.9176 (mtpt) cc_final: 0.8880 (ttmt) REVERT: k 104 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: E 4 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8291 (mp0) REVERT: E 6 LYS cc_start: 0.8996 (tttt) cc_final: 0.8725 (tttp) REVERT: r 104 GLU cc_start: 0.8703 (mp0) cc_final: 0.8423 (mp0) REVERT: u 404 GLU cc_start: 0.8858 (mp0) cc_final: 0.8382 (mp0) REVERT: u 406 LYS cc_start: 0.9050 (mptt) cc_final: 0.8666 (ttmt) REVERT: F 7 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.8278 (m-10) REVERT: y 104 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: y 107 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: z 206 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8848 (ttpt) REVERT: z 207 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8211 (m-10) REVERT: 0 307 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: G 6 LYS cc_start: 0.9371 (tttt) cc_final: 0.8832 (tttm) REVERT: G 7 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.7810 (m-10) REVERT: 6 206 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8857 (ttpt) REVERT: 6 207 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8133 (m-10) REVERT: H 4 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: H 6 LYS cc_start: 0.9312 (tttt) cc_final: 0.8860 (tttp) REVERT: EA 302 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8818 (ttmm) REVERT: JA 104 GLU cc_start: 0.4621 (OUTLIER) cc_final: 0.3760 (pm20) REVERT: J 4 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7924 (tm-30) REVERT: QA 104 GLU cc_start: 0.8934 (pm20) cc_final: 0.7647 (mm-30) REVERT: TA 404 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8006 (tm-30) REVERT: a 3 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8487 (t80) REVERT: a 4 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: a 6 LYS cc_start: 0.9335 (tttp) cc_final: 0.9106 (tttp) REVERT: XA 52 LYS cc_start: 0.9032 (tmtt) cc_final: 0.8755 (tmtt) REVERT: XA 55 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7840 (t80) REVERT: XA 56 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8972 (tttp) REVERT: YA 103 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8011 (t80) REVERT: YA 104 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: ZA 155 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8073 (t80) REVERT: ZA 156 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9139 (tttp) REVERT: aA 203 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8116 (t80) REVERT: bA 255 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7751 (t80) REVERT: cA 304 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: dA 355 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7656 (t80) REVERT: eA 403 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8509 (t80) REVERT: eA 404 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8080 (tm-30) REVERT: fA 455 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8106 (t80) REVERT: fA 456 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9134 (tttm) REVERT: mA 56 LYS cc_start: 0.9318 (tttt) cc_final: 0.9095 (tttp) REVERT: oA 156 LYS cc_start: 0.9370 (tmtt) cc_final: 0.9102 (tttp) REVERT: rA 304 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: rA 305 PHE cc_start: 0.8957 (t80) cc_final: 0.8630 (t80) REVERT: sA 355 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7263 (t80) REVERT: uA 456 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9118 (tttp) REVERT: c 5 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8220 (t80) REVERT: 1A 56 LYS cc_start: 0.9396 (tmtt) cc_final: 0.9065 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8514 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9356 (tmtt) cc_final: 0.9021 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8174 (t80) REVERT: 4A 206 LYS cc_start: 0.9226 (tttm) cc_final: 0.8802 (tttm) REVERT: 5A 256 LYS cc_start: 0.9271 (tmtt) cc_final: 0.9003 (tttm) REVERT: 6A 302 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8897 (tmtt) REVERT: 7A 355 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7885 (t80) REVERT: 7A 356 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9015 (tttm) REVERT: 9A 456 LYS cc_start: 0.9193 (tttm) cc_final: 0.8672 (tmtt) REVERT: d 5 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8392 (t80) REVERT: GB 56 LYS cc_start: 0.9351 (tmtt) cc_final: 0.9045 (tmtt) REVERT: HB 105 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.8337 (t80) REVERT: JB 205 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7971 (t80) REVERT: KB 256 LYS cc_start: 0.9145 (tmtt) cc_final: 0.8857 (tmtt) REVERT: LB 302 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8893 (ttmm) REVERT: LB 306 LYS cc_start: 0.9359 (tttm) cc_final: 0.9121 (tttm) REVERT: MB 356 LYS cc_start: 0.9093 (tmtt) cc_final: 0.8861 (tmtt) REVERT: VB 52 LYS cc_start: 0.9010 (tmtt) cc_final: 0.8460 (pptt) REVERT: XB 152 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8518 (pptt) REVERT: XB 157 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7599 (t80) REVERT: YB 205 PHE cc_start: 0.9046 (t80) cc_final: 0.8822 (t80) REVERT: ZB 252 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8506 (pptt) REVERT: aB 304 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: bB 352 LYS cc_start: 0.9123 (tmtt) cc_final: 0.8400 (pptt) REVERT: dB 452 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8338 (pptt) outliers start: 131 outliers final: 75 residues processed: 357 average time/residue: 0.1819 time to fit residues: 77.8713 Evaluate side-chains 446 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 319 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 406 LYS Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 302 LYS Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain SA residue 304 GLU Chi-restraints excluded: chain TA residue 406 LYS Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 302 LYS Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 402 LYS Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 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 = 0.3411 r_free = 0.3411 target = 0.079930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072307 restraints weight = 23421.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.074140 restraints weight = 9091.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.075339 restraints weight = 4631.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076141 restraints weight = 2746.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076738 restraints weight = 1826.319| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.152 8700 Z= 2.307 Angle : 2.739 20.695 11300 Z= 1.316 Chirality : 0.138 0.390 800 Planarity : 0.011 0.045 1500 Dihedral : 26.095 89.636 1021 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 118.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.50 % Favored : 74.50 % Rotamer: Outliers : 22.50 % Allowed : 29.50 % Favored : 48.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.06 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.103 0.011 PHEcA 303 Details of bonding type rmsd covalent geometry : bond 0.05098 ( 8700) covalent geometry : angle 2.73946 (11300) hydrogen bonds : bond 0.12157 ( 139) hydrogen bonds : angle 8.86466 ( 381) =============================================================================== Job complete usr+sys time: 1483.37 seconds wall clock time: 26 minutes 40.84 seconds (1600.84 seconds total)