Starting phenix.real_space_refine on Thu Mar 13 01:25:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqi_23487/03_2025/7lqi_23487.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqi_23487/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqi_23487/03_2025/7lqi_23487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqi_23487/03_2025/7lqi_23487.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqi_23487/03_2025/7lqi_23487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqi_23487/03_2025/7lqi_23487.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.11, per 1000 atoms: 0.61 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: 2.10 Conformation dependent library (CDL) restraints added in 576.4 milliseconds 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: 1.53 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: 2.20 Time building geometry restraints manager: 2.42 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: 2.970 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.280 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- 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= 0.861 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 : 22.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 : 0.910 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: 0.4090 time to fit residues: 179.6611 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 : 1.196 ------------------------------------------------------------------------------- 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 = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068097 restraints weight = 23674.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.069832 restraints weight = 9252.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.071004 restraints weight = 4799.868| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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= 2.767 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 : 115.74 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: A 6 LYS cc_start: 0.9079 (tttt) cc_final: 0.8690 (tttm) REVERT: A 7 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: K 104 GLU cc_start: 0.8625 (mp0) cc_final: 0.8275 (mp0) REVERT: K 107 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.8443 (m-80) REVERT: L 207 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: M 306 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8635 (tttt) REVERT: M 307 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8052 (m-10) REVERT: B 4 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: T 306 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8721 (ttmt) REVERT: C 4 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8542 (mp0) REVERT: C 6 LYS cc_start: 0.8981 (tttt) cc_final: 0.8626 (tttm) REVERT: D 4 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7851 (tm-30) REVERT: m 304 GLU cc_start: 0.8644 (mp0) cc_final: 0.7896 (mp0) REVERT: n 404 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7965 (mt-10) REVERT: E 4 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: E 6 LYS cc_start: 0.9077 (tttt) cc_final: 0.8731 (tttp) REVERT: r 104 GLU cc_start: 0.8608 (mp0) cc_final: 0.8232 (mp0) REVERT: u 404 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7957 (mm-30) REVERT: u 406 LYS cc_start: 0.8971 (mptt) cc_final: 0.8581 (ttmt) REVERT: F 4 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: F 7 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8308 (m-10) REVERT: y 104 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7771 (tm-30) REVERT: y 107 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: z 207 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8186 (m-10) REVERT: 0 307 PHE cc_start: 0.9366 (OUTLIER) cc_final: 0.8573 (m-80) REVERT: G 6 LYS cc_start: 0.9373 (tttt) cc_final: 0.8800 (tttm) REVERT: G 7 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.7897 (m-10) REVERT: 6 207 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8064 (m-10) REVERT: 7 307 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: H 4 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7564 (tm-30) REVERT: H 6 LYS cc_start: 0.9351 (tttt) cc_final: 0.8944 (ttmt) REVERT: I 6 LYS cc_start: 0.9120 (tttt) cc_final: 0.8789 (tttm) REVERT: KA 204 GLU cc_start: 0.8556 (mp0) cc_final: 0.8348 (pm20) REVERT: LA 304 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8332 (pm20) REVERT: QA 104 GLU cc_start: 0.8880 (pm20) cc_final: 0.8595 (pm20) REVERT: RA 204 GLU cc_start: 0.8914 (pm20) cc_final: 0.8597 (pm20) REVERT: SA 304 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: TA 404 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7596 (tm-30) REVERT: XA 55 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7794 (t80) REVERT: XA 56 LYS cc_start: 0.9111 (tmtt) cc_final: 0.8883 (tttm) REVERT: ZA 155 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8015 (t80) REVERT: ZA 156 LYS cc_start: 0.9353 (tmtt) cc_final: 0.9027 (tmtt) REVERT: aA 203 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.6849 (t80) REVERT: aA 204 GLU cc_start: 0.8407 (tp30) cc_final: 0.7880 (tm-30) REVERT: aA 206 LYS cc_start: 0.9128 (tttm) cc_final: 0.8863 (tttp) REVERT: bA 255 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7788 (t80) REVERT: bA 256 LYS cc_start: 0.9143 (tmtt) cc_final: 0.8920 (tmtt) REVERT: cA 302 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8785 (tmtt) REVERT: cA 303 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.6385 (t80) REVERT: cA 304 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: dA 355 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7646 (t80) REVERT: dA 356 LYS cc_start: 0.8994 (tmtt) cc_final: 0.8682 (tttm) REVERT: eA 406 LYS cc_start: 0.9364 (tttp) cc_final: 0.9137 (tttp) REVERT: fA 455 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8028 (t80) REVERT: fA 456 LYS cc_start: 0.9376 (tmtt) cc_final: 0.9128 (tttm) REVERT: b 2 LYS cc_start: 0.9217 (ttmm) cc_final: 0.8992 (ttmm) REVERT: mA 55 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7263 (t80) REVERT: mA 56 LYS cc_start: 0.9331 (tmtt) cc_final: 0.9115 (tttp) REVERT: oA 155 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7184 (t80) REVERT: oA 156 LYS cc_start: 0.9331 (tmtt) cc_final: 0.9042 (tttp) REVERT: pA 204 GLU cc_start: 0.8595 (tp30) cc_final: 0.8246 (tm-30) REVERT: qA 255 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.6848 (t80) REVERT: rA 302 LYS cc_start: 0.9140 (tmtt) cc_final: 0.8911 (tmtt) REVERT: rA 304 GLU cc_start: 0.8539 (tp30) cc_final: 0.8311 (tp30) REVERT: sA 355 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.6802 (t80) REVERT: tA 406 LYS cc_start: 0.9320 (tttp) cc_final: 0.8914 (tttp) REVERT: uA 455 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7218 (t80) REVERT: uA 456 LYS cc_start: 0.9380 (tmtt) cc_final: 0.9102 (tttp) REVERT: c 4 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8390 (tm-30) REVERT: 1A 56 LYS cc_start: 0.9323 (tmtt) cc_final: 0.9057 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8296 (tm-30) REVERT: 3A 152 LYS cc_start: 0.9180 (tmtt) cc_final: 0.8860 (tmtt) REVERT: 3A 156 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9022 (tmtt) REVERT: 4A 206 LYS cc_start: 0.9027 (tttm) cc_final: 0.8714 (tttm) REVERT: 5A 256 LYS cc_start: 0.9123 (tmtt) cc_final: 0.8880 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9334 (tmtt) cc_final: 0.8644 (tmtt) REVERT: GB 56 LYS cc_start: 0.9332 (tmtt) cc_final: 0.8991 (tmtt) REVERT: LB 302 LYS cc_start: 0.9197 (tmtt) cc_final: 0.8809 (ttmm) REVERT: OB 456 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9151 (tmtt) REVERT: e 4 GLU cc_start: 0.8700 (tp30) cc_final: 0.8238 (tm-30) REVERT: VB 55 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7776 (t80) REVERT: XB 157 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7799 (t80) REVERT: YB 204 GLU cc_start: 0.8599 (tp30) cc_final: 0.8228 (tm-30) REVERT: aB 302 LYS cc_start: 0.9165 (tmtt) cc_final: 0.8649 (tmtt) REVERT: cB 402 LYS cc_start: 0.9148 (tmtt) cc_final: 0.8733 (ttmm) outliers start: 98 outliers final: 40 residues processed: 351 average time/residue: 0.3984 time to fit residues: 166.4553 Evaluate side-chains 386 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 312 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 GB residue 55 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 = 0.3317 r_free = 0.3317 target = 0.076949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069325 restraints weight = 23875.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071110 restraints weight = 9646.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072287 restraints weight = 5037.107| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.180 8700 Z= 2.758 Angle : 2.729 17.053 11300 Z= 1.310 Chirality : 0.136 0.332 800 Planarity : 0.011 0.041 1500 Dihedral : 26.856 88.385 1021 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 120.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.00 % Favored : 77.00 % Rotamer: Outliers : 18.50 % Allowed : 29.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (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 *********************** 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 427 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 316 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: A 6 LYS cc_start: 0.9092 (tttt) cc_final: 0.8732 (tttm) REVERT: A 7 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: K 104 GLU cc_start: 0.8627 (mp0) cc_final: 0.8418 (mp0) REVERT: K 107 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: L 207 PHE cc_start: 0.9304 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: M 306 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8720 (ttpt) REVERT: M 307 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: B 4 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: C 4 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: C 6 LYS cc_start: 0.9104 (tttt) cc_final: 0.8728 (tttm) REVERT: k 104 GLU cc_start: 0.8841 (mp0) cc_final: 0.8623 (mp0) REVERT: E 4 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: E 6 LYS cc_start: 0.9050 (tttt) cc_final: 0.8765 (tttp) REVERT: r 104 GLU cc_start: 0.8667 (mp0) cc_final: 0.8372 (mp0) REVERT: u 404 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7826 (mm-30) REVERT: u 406 LYS cc_start: 0.9039 (mptt) cc_final: 0.8601 (ttmt) REVERT: F 7 PHE cc_start: 0.9419 (OUTLIER) cc_final: 0.8293 (m-10) REVERT: y 107 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: z 206 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8867 (ttpt) REVERT: z 207 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: 0 307 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.8624 (m-80) REVERT: 1 404 GLU cc_start: 0.8887 (mp0) cc_final: 0.8635 (mp0) REVERT: G 6 LYS cc_start: 0.9441 (tttt) cc_final: 0.8885 (tttm) REVERT: G 7 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.7866 (m-10) REVERT: 6 206 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8780 (ttpt) REVERT: 6 207 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8082 (m-10) REVERT: H 4 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7783 (tm-30) REVERT: H 6 LYS cc_start: 0.9341 (tttt) cc_final: 0.8905 (ttmt) REVERT: I 6 LYS cc_start: 0.9061 (tttt) cc_final: 0.8758 (tttm) REVERT: KA 204 GLU cc_start: 0.8659 (mp0) cc_final: 0.8410 (pm20) REVERT: J 4 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7789 (tm-30) REVERT: QA 104 GLU cc_start: 0.8869 (pm20) cc_final: 0.8470 (pm20) REVERT: RA 204 GLU cc_start: 0.9013 (pm20) cc_final: 0.8703 (pm20) REVERT: SA 304 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: TA 404 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7852 (tm-30) REVERT: a 4 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: XA 55 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7895 (t80) REVERT: XA 56 LYS cc_start: 0.9216 (tmtt) cc_final: 0.8900 (tttp) REVERT: YA 104 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: ZA 155 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7966 (t80) REVERT: ZA 156 LYS cc_start: 0.9403 (tmtt) cc_final: 0.9165 (tttm) REVERT: aA 206 LYS cc_start: 0.9144 (tttm) cc_final: 0.8408 (tttp) REVERT: bA 255 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7780 (t80) REVERT: bA 256 LYS cc_start: 0.9256 (tmtt) cc_final: 0.8930 (tmtt) REVERT: cA 303 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.6697 (t80) REVERT: cA 304 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: dA 355 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7677 (t80) REVERT: dA 356 LYS cc_start: 0.9182 (tmtt) cc_final: 0.8826 (tttp) REVERT: eA 403 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.7378 (t80) REVERT: eA 406 LYS cc_start: 0.9403 (tttp) cc_final: 0.9192 (tttp) REVERT: fA 455 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8073 (t80) REVERT: fA 456 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9067 (tttp) REVERT: mA 55 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7268 (t80) REVERT: mA 56 LYS cc_start: 0.9386 (tmtt) cc_final: 0.9131 (tttp) REVERT: oA 156 LYS cc_start: 0.9329 (tmtt) cc_final: 0.9083 (tttp) REVERT: qA 252 LYS cc_start: 0.8980 (tmtt) cc_final: 0.8774 (tmtt) REVERT: sA 355 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.6902 (t80) REVERT: sA 356 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8790 (tttm) REVERT: uA 455 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.6896 (t80) REVERT: uA 456 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9059 (tttp) REVERT: c 4 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8129 (tm-30) REVERT: 1A 56 LYS cc_start: 0.9390 (tmtt) cc_final: 0.9057 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8442 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9326 (tmtt) cc_final: 0.8942 (tmtt) REVERT: 4A 204 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7719 (tm-30) REVERT: 4A 206 LYS cc_start: 0.9132 (tttm) cc_final: 0.8864 (tttm) REVERT: 7A 356 LYS cc_start: 0.9364 (tmtt) cc_final: 0.8820 (tmtt) REVERT: GB 56 LYS cc_start: 0.9351 (tmtt) cc_final: 0.9124 (tmtt) REVERT: JB 204 GLU cc_start: 0.8652 (tp30) cc_final: 0.8197 (pm20) REVERT: KB 256 LYS cc_start: 0.9139 (tmtt) cc_final: 0.8790 (tmtt) REVERT: LB 302 LYS cc_start: 0.9184 (tmtt) cc_final: 0.8811 (ttmm) REVERT: LB 305 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8272 (t80) REVERT: OB 456 LYS cc_start: 0.9325 (tmtt) cc_final: 0.9106 (tttm) REVERT: VB 55 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7734 (t80) REVERT: XB 155 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7766 (t80) REVERT: XB 157 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7496 (t80) REVERT: YB 204 GLU cc_start: 0.8528 (tp30) cc_final: 0.8102 (tm-30) REVERT: aB 302 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8540 (ttmm) REVERT: aB 305 PHE cc_start: 0.8899 (t80) cc_final: 0.8690 (t80) REVERT: bB 352 LYS cc_start: 0.9011 (tmtt) cc_final: 0.8521 (pptt) REVERT: cB 402 LYS cc_start: 0.9139 (tmtt) cc_final: 0.8762 (ttmm) outliers start: 111 outliers final: 56 residues processed: 341 average time/residue: 0.3894 time to fit residues: 158.3013 Evaluate side-chains 407 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 314 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 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 = 0.3400 r_free = 0.3400 target = 0.079551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.071987 restraints weight = 23416.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.073817 restraints weight = 8979.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.074989 restraints weight = 4564.645| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.157 8700 Z= 2.764 Angle : 2.729 18.264 11300 Z= 1.311 Chirality : 0.137 0.336 800 Planarity : 0.011 0.039 1500 Dihedral : 26.655 89.665 1021 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 118.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.00 % Favored : 76.00 % Rotamer: Outliers : 19.50 % Allowed : 31.17 % Favored : 49.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (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 *********************** 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 436 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 319 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: A 6 LYS cc_start: 0.9087 (tttt) cc_final: 0.8660 (tttm) REVERT: A 7 PHE cc_start: 0.9432 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: K 104 GLU cc_start: 0.8635 (mp0) cc_final: 0.8411 (mp0) REVERT: K 107 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.8508 (m-80) REVERT: L 207 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8912 (m-80) REVERT: M 306 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8625 (tttt) REVERT: M 307 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.8111 (m-10) REVERT: B 4 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: C 4 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8534 (mp0) REVERT: C 6 LYS cc_start: 0.9135 (tttt) cc_final: 0.8904 (ttmt) REVERT: Y 106 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8844 (ttmt) REVERT: k 104 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: m 304 GLU cc_start: 0.8686 (mp0) cc_final: 0.8433 (mp0) REVERT: E 4 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: E 6 LYS cc_start: 0.9037 (tttt) cc_final: 0.8766 (tttp) REVERT: r 104 GLU cc_start: 0.8663 (mp0) cc_final: 0.8378 (mp0) REVERT: u 404 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8084 (mm-30) REVERT: u 406 LYS cc_start: 0.8996 (mptt) cc_final: 0.8593 (ttmt) REVERT: F 7 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.8327 (m-10) REVERT: y 104 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7842 (tm-30) REVERT: y 107 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8455 (m-80) REVERT: z 206 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8862 (ttpt) REVERT: z 207 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: 0 307 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: G 6 LYS cc_start: 0.9435 (tttt) cc_final: 0.8884 (tttm) REVERT: G 7 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.7829 (m-10) REVERT: 6 206 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8809 (ttpt) REVERT: 6 207 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8103 (m-10) REVERT: H 4 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: H 6 LYS cc_start: 0.9338 (tttt) cc_final: 0.8910 (ttmt) REVERT: I 6 LYS cc_start: 0.9040 (tttt) cc_final: 0.8749 (tttm) REVERT: JA 104 GLU cc_start: 0.4618 (OUTLIER) cc_final: 0.3756 (pm20) REVERT: J 4 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: RA 204 GLU cc_start: 0.9028 (pm20) cc_final: 0.8681 (pm20) REVERT: TA 404 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7914 (tm-30) REVERT: a 3 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.7584 (t80) REVERT: a 4 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: XA 52 LYS cc_start: 0.9105 (tmtt) cc_final: 0.8856 (tmtt) REVERT: XA 55 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7881 (t80) REVERT: XA 56 LYS cc_start: 0.9263 (tmtt) cc_final: 0.8925 (tttp) REVERT: YA 104 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: ZA 152 LYS cc_start: 0.9061 (tmtt) cc_final: 0.8860 (tmtt) REVERT: ZA 155 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7968 (t80) REVERT: ZA 156 LYS cc_start: 0.9404 (tmtt) cc_final: 0.9172 (tttm) REVERT: aA 203 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.8299 (t80) REVERT: aA 206 LYS cc_start: 0.9156 (tttm) cc_final: 0.8595 (tttp) REVERT: bA 255 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7886 (t80) REVERT: cA 302 LYS cc_start: 0.9213 (tmtt) cc_final: 0.9007 (tmtt) REVERT: cA 303 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.6884 (t80) REVERT: cA 304 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: dA 355 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7626 (t80) REVERT: eA 403 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.7185 (t80) REVERT: eA 406 LYS cc_start: 0.9418 (tttp) cc_final: 0.9218 (tttp) REVERT: fA 452 LYS cc_start: 0.9121 (tmtt) cc_final: 0.8895 (tmtt) REVERT: fA 455 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.8029 (t80) REVERT: fA 456 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9117 (tttm) REVERT: mA 55 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.6991 (t80) REVERT: mA 56 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9107 (tttp) REVERT: oA 156 LYS cc_start: 0.9343 (tmtt) cc_final: 0.9083 (tttp) REVERT: qA 256 LYS cc_start: 0.9219 (tmtt) cc_final: 0.8862 (tmtt) REVERT: rA 304 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: rA 305 PHE cc_start: 0.8907 (t80) cc_final: 0.8459 (t80) REVERT: sA 355 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.6910 (t80) REVERT: sA 356 LYS cc_start: 0.9064 (tmtt) cc_final: 0.8781 (tttm) REVERT: uA 455 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.6878 (t80) REVERT: uA 456 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9073 (tttp) REVERT: 1A 56 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9015 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: 4A 205 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8134 (t80) REVERT: 4A 206 LYS cc_start: 0.9194 (tttm) cc_final: 0.8862 (tttm) REVERT: 5A 256 LYS cc_start: 0.9178 (tmtt) cc_final: 0.8782 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9087 (tttm) REVERT: GB 56 LYS cc_start: 0.9359 (tmtt) cc_final: 0.9089 (tmtt) REVERT: JB 204 GLU cc_start: 0.8672 (tp30) cc_final: 0.8159 (pm20) REVERT: LB 302 LYS cc_start: 0.9173 (tmtt) cc_final: 0.8853 (ttmm) REVERT: LB 305 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8288 (t80) REVERT: LB 306 LYS cc_start: 0.9376 (tttm) cc_final: 0.9050 (tttm) REVERT: OB 456 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9114 (tttm) REVERT: XB 152 LYS cc_start: 0.8967 (tmtt) cc_final: 0.8518 (pptt) REVERT: XB 155 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7766 (t80) REVERT: XB 157 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7501 (t80) REVERT: YB 205 PHE cc_start: 0.8958 (t80) cc_final: 0.8677 (t80) REVERT: ZB 252 LYS cc_start: 0.9153 (tmtt) cc_final: 0.8448 (pptt) REVERT: ZB 256 LYS cc_start: 0.9327 (tmtt) cc_final: 0.9092 (tttp) REVERT: aB 305 PHE cc_start: 0.8946 (t80) cc_final: 0.8744 (t80) REVERT: bB 352 LYS cc_start: 0.9094 (tmtt) cc_final: 0.8496 (pptt) REVERT: cB 402 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8739 (ttmm) REVERT: dB 452 LYS cc_start: 0.9083 (tmtt) cc_final: 0.8434 (pptt) outliers start: 117 outliers final: 60 residues processed: 349 average time/residue: 0.4416 time to fit residues: 183.6744 Evaluate side-chains 423 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 318 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 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 JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS 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 = 0.3408 r_free = 0.3408 target = 0.079983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072413 restraints weight = 23358.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.074235 restraints weight = 8926.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.075375 restraints weight = 4516.681| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.171 8700 Z= 2.762 Angle : 2.727 19.297 11300 Z= 1.310 Chirality : 0.137 0.341 800 Planarity : 0.011 0.039 1500 Dihedral : 26.525 89.775 1021 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 116.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.75 % Favored : 75.25 % Rotamer: Outliers : 21.00 % Allowed : 30.17 % Favored : 48.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.091 0.011 PHEaA 203 *********************** 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 445 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 319 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8416 (mp0) REVERT: A 6 LYS cc_start: 0.9080 (tttt) cc_final: 0.8744 (tttm) REVERT: A 7 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: K 104 GLU cc_start: 0.8645 (mp0) cc_final: 0.8395 (mp0) REVERT: K 107 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.8489 (m-80) REVERT: L 207 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.8963 (m-80) REVERT: M 306 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8643 (tttt) REVERT: M 307 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.8084 (m-10) REVERT: B 4 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8473 (mp0) REVERT: U 404 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7758 (mm-30) REVERT: C 4 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: C 6 LYS cc_start: 0.9163 (tttt) cc_final: 0.8927 (ttmt) REVERT: Y 106 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8855 (ttmt) REVERT: D 4 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7898 (tm-30) REVERT: k 104 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: E 4 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8242 (mp0) REVERT: E 6 LYS cc_start: 0.9042 (tttt) cc_final: 0.8758 (tttp) REVERT: r 104 GLU cc_start: 0.8694 (mp0) cc_final: 0.8420 (mp0) REVERT: u 404 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8052 (mm-30) REVERT: u 406 LYS cc_start: 0.8962 (mptt) cc_final: 0.8505 (ttmt) REVERT: F 7 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.8234 (m-10) REVERT: y 104 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7827 (tm-30) REVERT: y 107 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.8437 (m-80) REVERT: z 206 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8856 (ttpt) REVERT: z 207 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.8212 (m-10) REVERT: 0 307 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.8604 (m-80) REVERT: G 6 LYS cc_start: 0.9417 (tttt) cc_final: 0.8871 (tttm) REVERT: G 7 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.7824 (m-10) REVERT: 6 206 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8843 (ttpt) REVERT: 6 207 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8107 (m-10) REVERT: H 4 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: H 6 LYS cc_start: 0.9345 (tttt) cc_final: 0.8909 (ttmt) REVERT: I 6 LYS cc_start: 0.9040 (tttt) cc_final: 0.8759 (tttm) REVERT: JA 104 GLU cc_start: 0.4651 (OUTLIER) cc_final: 0.3784 (pm20) REVERT: J 4 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: RA 204 GLU cc_start: 0.9021 (pm20) cc_final: 0.8655 (pm20) REVERT: TA 404 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7989 (tm-30) REVERT: a 3 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.7611 (t80) REVERT: a 4 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7983 (tp30) REVERT: XA 52 LYS cc_start: 0.9061 (tmtt) cc_final: 0.8783 (tmtt) REVERT: XA 55 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7832 (t80) REVERT: XA 56 LYS cc_start: 0.9263 (tmtt) cc_final: 0.8920 (tttp) REVERT: YA 103 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8154 (t80) REVERT: YA 104 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: ZA 155 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8044 (t80) REVERT: ZA 156 LYS cc_start: 0.9395 (tmtt) cc_final: 0.9139 (tttm) REVERT: aA 203 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8332 (t80) REVERT: cA 303 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.7103 (t80) REVERT: cA 304 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: dA 355 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7664 (t80) REVERT: eA 403 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8438 (t80) REVERT: eA 404 GLU cc_start: 0.8588 (tm-30) cc_final: 0.7882 (tm-30) REVERT: eA 406 LYS cc_start: 0.9418 (tttp) cc_final: 0.9195 (tttp) REVERT: fA 452 LYS cc_start: 0.9110 (tmtt) cc_final: 0.8908 (tmtt) REVERT: fA 455 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8129 (t80) REVERT: fA 456 LYS cc_start: 0.9371 (OUTLIER) cc_final: 0.9114 (tttm) REVERT: mA 55 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.6996 (t80) REVERT: mA 56 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9083 (tttp) REVERT: oA 152 LYS cc_start: 0.8975 (tmtt) cc_final: 0.8711 (tmtt) REVERT: oA 156 LYS cc_start: 0.9344 (tmtt) cc_final: 0.9087 (tttp) REVERT: qA 256 LYS cc_start: 0.9213 (tmtt) cc_final: 0.8689 (tmtt) REVERT: rA 304 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8143 (tp30) REVERT: rA 305 PHE cc_start: 0.8926 (t80) cc_final: 0.8631 (t80) REVERT: sA 355 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7089 (t80) REVERT: sA 356 LYS cc_start: 0.9050 (tmtt) cc_final: 0.8702 (tttp) REVERT: uA 456 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9131 (tttp) REVERT: 1A 56 LYS cc_start: 0.9379 (tmtt) cc_final: 0.9010 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9049 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8187 (t80) REVERT: 4A 206 LYS cc_start: 0.9194 (tttm) cc_final: 0.8747 (tttm) REVERT: 7A 356 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9074 (tttm) REVERT: d 5 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8450 (t80) REVERT: JB 204 GLU cc_start: 0.8717 (tp30) cc_final: 0.8139 (pm20) REVERT: KB 256 LYS cc_start: 0.9136 (tmtt) cc_final: 0.8803 (tmtt) REVERT: LB 302 LYS cc_start: 0.9209 (tmtt) cc_final: 0.8899 (ttmm) REVERT: OB 456 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9124 (tttm) REVERT: VB 52 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8439 (pptt) REVERT: XB 152 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8525 (pptt) REVERT: XB 157 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7691 (t80) REVERT: YB 205 PHE cc_start: 0.8989 (t80) cc_final: 0.8623 (t80) REVERT: ZB 252 LYS cc_start: 0.9074 (tmtt) cc_final: 0.8438 (pptt) REVERT: bB 352 LYS cc_start: 0.9106 (tmtt) cc_final: 0.8491 (pptt) REVERT: cB 402 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8723 (ttmm) REVERT: dB 452 LYS cc_start: 0.9103 (tmtt) cc_final: 0.8448 (pptt) outliers start: 126 outliers final: 69 residues processed: 356 average time/residue: 0.4119 time to fit residues: 174.4492 Evaluate side-chains 431 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 318 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 U residue 404 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 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=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 = 0.3413 r_free = 0.3413 target = 0.080053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.072420 restraints weight = 23100.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.074248 restraints weight = 8926.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075424 restraints weight = 4580.360| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.158 8700 Z= 2.761 Angle : 2.726 19.887 11300 Z= 1.309 Chirality : 0.138 0.344 800 Planarity : 0.011 0.041 1500 Dihedral : 26.349 89.873 1021 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 116.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.75 % Favored : 74.25 % Rotamer: Outliers : 21.17 % Allowed : 30.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.094 0.011 PHEaA 203 *********************** 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 444 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 317 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: A 6 LYS cc_start: 0.9068 (tttt) cc_final: 0.8730 (tttm) REVERT: A 7 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: K 104 GLU cc_start: 0.8650 (mp0) cc_final: 0.8386 (mp0) REVERT: K 107 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8487 (m-80) REVERT: L 207 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.8967 (m-80) REVERT: M 304 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: M 306 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8665 (tttt) REVERT: M 307 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.8002 (m-10) REVERT: B 4 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: U 404 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: C 4 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: C 6 LYS cc_start: 0.9181 (tttt) cc_final: 0.8799 (tttm) REVERT: Y 106 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8873 (ttmt) REVERT: D 4 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: k 104 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: E 4 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: E 6 LYS cc_start: 0.9029 (tttt) cc_final: 0.8748 (tttp) REVERT: r 104 GLU cc_start: 0.8679 (mp0) cc_final: 0.8404 (mp0) REVERT: u 406 LYS cc_start: 0.8954 (mptt) cc_final: 0.8553 (ttmt) REVERT: F 7 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8315 (m-10) REVERT: y 104 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7909 (tm-30) REVERT: y 107 PHE cc_start: 0.9372 (OUTLIER) cc_final: 0.8440 (m-80) REVERT: z 206 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8857 (ttpt) REVERT: z 207 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: 0 307 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: G 6 LYS cc_start: 0.9432 (tttt) cc_final: 0.8894 (tttm) REVERT: G 7 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.7807 (m-10) REVERT: 6 206 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8849 (ttpt) REVERT: 6 207 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8113 (m-10) REVERT: H 4 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: H 6 LYS cc_start: 0.9328 (tttt) cc_final: 0.8892 (ttmt) REVERT: JA 104 GLU cc_start: 0.4683 (OUTLIER) cc_final: 0.3820 (pm20) REVERT: J 4 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: QA 104 GLU cc_start: 0.8943 (pm20) cc_final: 0.7655 (mm-30) REVERT: RA 204 GLU cc_start: 0.9028 (pm20) cc_final: 0.8638 (pm20) REVERT: TA 404 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8023 (tm-30) REVERT: a 3 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.7598 (t80) REVERT: a 4 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: XA 52 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8743 (tmtt) REVERT: XA 55 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7835 (t80) REVERT: XA 56 LYS cc_start: 0.9260 (tmtt) cc_final: 0.8935 (tttp) REVERT: YA 103 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8139 (t80) REVERT: YA 104 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.7997 (tp30) REVERT: ZA 155 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8015 (t80) REVERT: ZA 156 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9153 (tttm) REVERT: aA 203 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8171 (t80) REVERT: bA 255 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7707 (t80) REVERT: cA 304 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8357 (tm-30) REVERT: dA 355 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7668 (t80) REVERT: eA 403 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8416 (t80) REVERT: eA 404 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7826 (tm-30) REVERT: eA 406 LYS cc_start: 0.9411 (tttp) cc_final: 0.9205 (tttp) REVERT: fA 452 LYS cc_start: 0.9103 (tmtt) cc_final: 0.8876 (tmtt) REVERT: fA 455 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8108 (t80) REVERT: fA 456 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.9133 (tttm) REVERT: mA 55 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.6981 (t80) REVERT: mA 56 LYS cc_start: 0.9340 (tmtt) cc_final: 0.9069 (tttp) REVERT: oA 152 LYS cc_start: 0.8980 (tmtt) cc_final: 0.8763 (tmtt) REVERT: oA 156 LYS cc_start: 0.9348 (tmtt) cc_final: 0.9081 (tttp) REVERT: qA 256 LYS cc_start: 0.9212 (tmtt) cc_final: 0.8975 (tttm) REVERT: rA 304 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: rA 305 PHE cc_start: 0.8924 (t80) cc_final: 0.8557 (t80) REVERT: sA 355 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7267 (t80) REVERT: sA 356 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8730 (tttm) REVERT: uA 456 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9113 (tttp) REVERT: 1A 56 LYS cc_start: 0.9408 (tmtt) cc_final: 0.9094 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8470 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9356 (tmtt) cc_final: 0.8976 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8138 (t80) REVERT: 4A 206 LYS cc_start: 0.9197 (tttm) cc_final: 0.8835 (tttm) REVERT: 5A 256 LYS cc_start: 0.9245 (tmtt) cc_final: 0.8905 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9062 (tttm) REVERT: 9A 456 LYS cc_start: 0.9180 (tttm) cc_final: 0.8845 (tmtt) REVERT: d 5 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.8474 (t80) REVERT: JB 204 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: KB 256 LYS cc_start: 0.9155 (tmtt) cc_final: 0.8818 (tmtt) REVERT: LB 302 LYS cc_start: 0.9205 (tmtt) cc_final: 0.8896 (ttmm) REVERT: LB 306 LYS cc_start: 0.9379 (tttm) cc_final: 0.9137 (tttm) REVERT: MB 356 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8864 (tmtt) REVERT: OB 456 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9113 (tttm) REVERT: VB 52 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8440 (pptt) REVERT: XB 152 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8517 (pptt) REVERT: XB 157 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7684 (t80) REVERT: ZB 252 LYS cc_start: 0.9164 (tmtt) cc_final: 0.8531 (pptt) REVERT: aB 304 GLU cc_start: 0.8745 (tp30) cc_final: 0.8169 (tm-30) REVERT: bB 352 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8568 (pptt) REVERT: dB 452 LYS cc_start: 0.9131 (tmtt) cc_final: 0.8454 (pptt) outliers start: 127 outliers final: 65 residues processed: 351 average time/residue: 0.3804 time to fit residues: 159.1270 Evaluate side-chains 429 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 315 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 404 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 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 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 sA residue 356 LYS 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 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 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 = 0.3417 r_free = 0.3417 target = 0.080095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.072425 restraints weight = 23353.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074264 restraints weight = 9036.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.075454 restraints weight = 4630.335| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.6782 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= 2.761 Angle : 2.729 20.341 11300 Z= 1.311 Chirality : 0.138 0.346 800 Planarity : 0.011 0.042 1500 Dihedral : 26.273 89.894 1021 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 116.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.50 % Favored : 74.50 % Rotamer: Outliers : 22.33 % Allowed : 30.33 % Favored : 47.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.18 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.098 0.011 PHEaA 203 *********************** 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 450 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 316 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: A 6 LYS cc_start: 0.9070 (tttt) cc_final: 0.8724 (tttm) REVERT: A 7 PHE cc_start: 0.9442 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: K 104 GLU cc_start: 0.8644 (mp0) cc_final: 0.8380 (mp0) REVERT: K 107 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.8485 (m-80) REVERT: L 207 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.8945 (m-80) REVERT: M 304 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: M 306 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8689 (tttt) REVERT: M 307 PHE cc_start: 0.9456 (OUTLIER) cc_final: 0.8004 (m-10) REVERT: B 4 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: U 404 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7813 (mm-30) REVERT: C 4 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: C 6 LYS cc_start: 0.9184 (tttt) cc_final: 0.8811 (tttp) REVERT: Y 106 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8880 (ttmt) REVERT: D 4 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: k 104 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8170 (mp0) REVERT: E 4 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: E 6 LYS cc_start: 0.9014 (tttt) cc_final: 0.8735 (tttp) REVERT: r 104 GLU cc_start: 0.8695 (mp0) cc_final: 0.8418 (mp0) REVERT: u 404 GLU cc_start: 0.8716 (mp0) cc_final: 0.8271 (mp0) REVERT: u 406 LYS cc_start: 0.9031 (mptt) cc_final: 0.8690 (ttmt) REVERT: F 7 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.8311 (m-10) REVERT: y 104 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7896 (tm-30) REVERT: y 107 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8447 (m-80) REVERT: z 206 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8864 (ttpt) REVERT: z 207 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8202 (m-10) REVERT: 0 307 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: G 6 LYS cc_start: 0.9429 (tttt) cc_final: 0.8928 (tttm) REVERT: G 7 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.7893 (m-10) REVERT: 6 206 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8855 (ttpt) REVERT: 6 207 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8109 (m-10) REVERT: H 4 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: H 6 LYS cc_start: 0.9327 (tttt) cc_final: 0.8885 (ttmt) REVERT: JA 104 GLU cc_start: 0.4693 (OUTLIER) cc_final: 0.3834 (pm20) REVERT: J 4 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: QA 104 GLU cc_start: 0.8931 (pm20) cc_final: 0.7659 (mm-30) REVERT: RA 204 GLU cc_start: 0.9032 (pm20) cc_final: 0.8647 (pm20) REVERT: SA 304 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8508 (mp0) REVERT: TA 404 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8014 (tm-30) REVERT: a 3 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.7536 (t80) REVERT: a 4 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7966 (tp30) REVERT: XA 52 LYS cc_start: 0.9033 (tmtt) cc_final: 0.8738 (tmtt) REVERT: XA 55 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7854 (t80) REVERT: XA 56 LYS cc_start: 0.9275 (tmtt) cc_final: 0.8944 (tttp) REVERT: YA 103 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8023 (t80) REVERT: YA 104 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: ZA 155 PHE cc_start: 0.8501 (OUTLIER) cc_final: 0.8066 (t80) REVERT: ZA 156 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9117 (tttp) REVERT: aA 203 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8218 (t80) REVERT: bA 255 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7874 (t80) REVERT: cA 303 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.7387 (t80) REVERT: cA 304 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: dA 355 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7675 (t80) REVERT: eA 403 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8497 (t80) REVERT: eA 404 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7974 (tm-30) REVERT: fA 455 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8144 (t80) REVERT: fA 456 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9134 (tttm) REVERT: mA 55 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.6992 (t80) REVERT: mA 56 LYS cc_start: 0.9316 (tmtt) cc_final: 0.8999 (tttp) REVERT: oA 156 LYS cc_start: 0.9352 (tmtt) cc_final: 0.9078 (tttp) REVERT: rA 304 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: rA 305 PHE cc_start: 0.8969 (t80) cc_final: 0.8633 (t80) REVERT: sA 355 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7120 (t80) REVERT: sA 356 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8762 (tttm) REVERT: uA 456 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9112 (tttp) REVERT: 1A 56 LYS cc_start: 0.9386 (tmtt) cc_final: 0.9047 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9351 (tmtt) cc_final: 0.8971 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8224 (t80) REVERT: 4A 206 LYS cc_start: 0.9202 (tttm) cc_final: 0.8778 (tttm) REVERT: 5A 256 LYS cc_start: 0.9243 (tmtt) cc_final: 0.8849 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9021 (tttm) REVERT: 9A 456 LYS cc_start: 0.9182 (tttm) cc_final: 0.8675 (tmtt) REVERT: d 5 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8473 (t80) REVERT: GB 56 LYS cc_start: 0.9354 (tmtt) cc_final: 0.9068 (tmtt) REVERT: JB 205 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8372 (t80) REVERT: KB 256 LYS cc_start: 0.9165 (tmtt) cc_final: 0.8846 (tmtt) REVERT: LB 302 LYS cc_start: 0.9207 (tmtt) cc_final: 0.8897 (ttmm) REVERT: LB 306 LYS cc_start: 0.9375 (tttm) cc_final: 0.9135 (tttm) REVERT: VB 52 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8445 (pptt) REVERT: XB 152 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8520 (pptt) REVERT: XB 157 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7656 (t80) REVERT: ZB 252 LYS cc_start: 0.9168 (tmtt) cc_final: 0.8539 (pptt) REVERT: aB 304 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: bB 352 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8435 (pptt) REVERT: dB 452 LYS cc_start: 0.9098 (tmtt) cc_final: 0.8447 (pptt) outliers start: 134 outliers final: 71 residues processed: 353 average time/residue: 0.3937 time to fit residues: 166.1970 Evaluate side-chains 438 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 316 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 306 LYS Chi-restraints excluded: chain U residue 404 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 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 J residue 6 LYS 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 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 sA residue 356 LYS 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 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 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 = 0.3412 r_free = 0.3412 target = 0.079901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.072343 restraints weight = 23541.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.074169 restraints weight = 9013.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.075350 restraints weight = 4585.902| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.6817 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= 2.762 Angle : 2.726 19.602 11300 Z= 1.310 Chirality : 0.138 0.349 800 Planarity : 0.011 0.042 1500 Dihedral : 26.216 89.748 1021 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 117.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 22.17 % Allowed : 30.67 % Favored : 47.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.098 0.011 PHEaA 203 *********************** 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 452 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 319 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8417 (mp0) REVERT: A 6 LYS cc_start: 0.9070 (tttt) cc_final: 0.8726 (tttm) REVERT: A 7 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: K 104 GLU cc_start: 0.8644 (mp0) cc_final: 0.8370 (mp0) REVERT: K 107 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: L 207 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8941 (m-80) REVERT: M 304 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: M 306 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8696 (tttt) REVERT: M 307 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.8002 (m-10) REVERT: B 4 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: U 404 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7851 (mm-30) REVERT: C 4 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8551 (mp0) REVERT: C 6 LYS cc_start: 0.9187 (tttt) cc_final: 0.8827 (tttm) REVERT: Y 106 LYS cc_start: 0.9170 (mtpt) cc_final: 0.8876 (ttmt) REVERT: k 104 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: E 4 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: E 6 LYS cc_start: 0.9013 (tttt) cc_final: 0.8733 (tttp) REVERT: r 104 GLU cc_start: 0.8701 (mp0) cc_final: 0.8423 (mp0) REVERT: u 404 GLU cc_start: 0.8767 (mp0) cc_final: 0.8526 (mp0) REVERT: u 406 LYS cc_start: 0.9034 (mptt) cc_final: 0.8663 (ttmt) REVERT: F 7 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.8302 (m-10) REVERT: y 104 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7874 (tm-30) REVERT: y 107 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8372 (m-80) REVERT: z 206 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8865 (ttpt) REVERT: z 207 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8193 (m-10) REVERT: 0 307 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.8608 (m-80) REVERT: G 6 LYS cc_start: 0.9432 (tttt) cc_final: 0.8888 (tttm) REVERT: G 7 PHE cc_start: 0.9302 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: 6 206 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8856 (ttpt) REVERT: 6 207 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: H 4 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: H 6 LYS cc_start: 0.9322 (tttt) cc_final: 0.8883 (ttmt) REVERT: EA 302 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8833 (ttmm) REVERT: JA 104 GLU cc_start: 0.4698 (OUTLIER) cc_final: 0.3847 (pm20) REVERT: J 4 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7958 (tm-30) REVERT: QA 104 GLU cc_start: 0.8938 (pm20) cc_final: 0.7658 (mm-30) REVERT: RA 204 GLU cc_start: 0.9036 (pm20) cc_final: 0.8642 (pm20) REVERT: TA 404 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8013 (tm-30) REVERT: a 3 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8485 (t80) REVERT: a 4 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: XA 52 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8738 (tmtt) REVERT: XA 55 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7850 (t80) REVERT: XA 56 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8945 (tttp) REVERT: YA 103 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8131 (t80) REVERT: YA 104 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: ZA 155 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8107 (t80) REVERT: ZA 156 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.9137 (tttp) REVERT: aA 203 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8255 (t80) REVERT: bA 255 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7878 (t80) REVERT: cA 303 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.7295 (t80) REVERT: cA 304 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8034 (tp30) REVERT: dA 355 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7663 (t80) REVERT: eA 403 PHE cc_start: 0.9130 (OUTLIER) cc_final: 0.8533 (t80) REVERT: eA 404 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8042 (tm-30) REVERT: fA 455 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8104 (t80) REVERT: fA 456 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9145 (tttm) REVERT: mA 56 LYS cc_start: 0.9315 (tmtt) cc_final: 0.9059 (tttp) REVERT: oA 156 LYS cc_start: 0.9363 (tmtt) cc_final: 0.9093 (tttp) REVERT: rA 304 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8127 (tp30) REVERT: rA 305 PHE cc_start: 0.8945 (t80) cc_final: 0.8654 (t80) REVERT: sA 355 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7075 (t80) REVERT: sA 356 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8762 (tttm) REVERT: uA 456 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9115 (tttp) REVERT: 1A 56 LYS cc_start: 0.9396 (tmtt) cc_final: 0.9100 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8508 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9354 (tmtt) cc_final: 0.8957 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8229 (t80) REVERT: 4A 206 LYS cc_start: 0.9207 (tttm) cc_final: 0.8781 (tttm) REVERT: 7A 356 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9013 (tttm) REVERT: 9A 456 LYS cc_start: 0.9157 (tttm) cc_final: 0.8627 (tmtt) REVERT: d 5 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8435 (t80) REVERT: GB 56 LYS cc_start: 0.9364 (tmtt) cc_final: 0.9058 (tmtt) REVERT: JB 205 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.7874 (t80) REVERT: LB 302 LYS cc_start: 0.9207 (tmtt) cc_final: 0.8894 (ttmm) REVERT: LB 306 LYS cc_start: 0.9369 (tttm) cc_final: 0.9127 (tttm) REVERT: VB 52 LYS cc_start: 0.9016 (tmtt) cc_final: 0.8457 (pptt) REVERT: XB 152 LYS cc_start: 0.9059 (tmtt) cc_final: 0.8516 (pptt) REVERT: XB 157 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7620 (t80) REVERT: YB 205 PHE cc_start: 0.9053 (t80) cc_final: 0.8808 (t80) REVERT: ZB 252 LYS cc_start: 0.9140 (tmtt) cc_final: 0.8471 (pptt) REVERT: aB 304 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: bB 352 LYS cc_start: 0.9139 (tmtt) cc_final: 0.8433 (pptt) REVERT: dB 452 LYS cc_start: 0.9097 (tmtt) cc_final: 0.8416 (pptt) outliers start: 133 outliers final: 73 residues processed: 356 average time/residue: 0.3969 time to fit residues: 169.3066 Evaluate side-chains 442 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 319 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 306 LYS Chi-restraints excluded: chain U residue 404 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 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 LA residue 306 LYS Chi-restraints excluded: chain MA residue 404 GLU Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 6 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 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 qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain sA residue 356 LYS 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 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 = 0.3426 r_free = 0.3426 target = 0.080892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073774 restraints weight = 24038.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075531 restraints weight = 8931.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.076625 restraints weight = 4453.035| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.6855 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= 2.763 Angle : 2.726 20.179 11300 Z= 1.310 Chirality : 0.138 0.367 800 Planarity : 0.011 0.041 1500 Dihedral : 26.176 89.677 1021 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 117.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 21.50 % Allowed : 30.83 % Favored : 47.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.08 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.094 0.011 PHEaA 203 *********************** 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 449 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 320 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8410 (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: 0.8361 (m-80) REVERT: K 104 GLU cc_start: 0.8635 (mp0) cc_final: 0.8356 (mp0) REVERT: K 107 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: L 207 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8971 (m-80) REVERT: M 304 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8209 (mp0) REVERT: M 306 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8692 (tttt) REVERT: M 307 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.8006 (m-10) REVERT: B 4 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: U 404 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: C 4 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8548 (mp0) REVERT: C 6 LYS cc_start: 0.9188 (tttt) cc_final: 0.8834 (tttm) REVERT: Y 106 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8878 (ttmt) REVERT: k 104 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: E 4 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: E 6 LYS cc_start: 0.9002 (tttt) cc_final: 0.8724 (tttp) REVERT: r 104 GLU cc_start: 0.8712 (mp0) cc_final: 0.8438 (mp0) REVERT: u 404 GLU cc_start: 0.8771 (mp0) cc_final: 0.8527 (mp0) REVERT: u 406 LYS cc_start: 0.9035 (mptt) cc_final: 0.8663 (ttmt) REVERT: F 7 PHE cc_start: 0.9430 (OUTLIER) cc_final: 0.8305 (m-10) REVERT: y 104 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7876 (tm-30) REVERT: y 107 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: z 206 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8848 (ttpt) REVERT: z 207 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8201 (m-10) REVERT: 0 307 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: G 6 LYS cc_start: 0.9418 (tttt) cc_final: 0.8897 (tttm) REVERT: G 7 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8021 (m-10) REVERT: 6 206 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8858 (ttpt) REVERT: 6 207 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.8125 (m-10) REVERT: H 4 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: H 6 LYS cc_start: 0.9313 (tttt) cc_final: 0.8862 (tttp) REVERT: EA 302 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8795 (ttmm) REVERT: JA 104 GLU cc_start: 0.4721 (OUTLIER) cc_final: 0.3872 (pm20) REVERT: J 4 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: QA 104 GLU cc_start: 0.8940 (pm20) cc_final: 0.7656 (mm-30) REVERT: RA 204 GLU cc_start: 0.9042 (pm20) cc_final: 0.8645 (pm20) REVERT: SA 304 GLU cc_start: 0.8928 (pm20) cc_final: 0.8425 (mp0) REVERT: TA 404 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8011 (tm-30) REVERT: a 3 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8488 (t80) REVERT: a 4 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: XA 52 LYS cc_start: 0.9028 (tmtt) cc_final: 0.8738 (tmtt) REVERT: XA 55 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7842 (t80) REVERT: XA 56 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8967 (tttp) REVERT: YA 104 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: ZA 155 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8113 (t80) REVERT: ZA 156 LYS cc_start: 0.9415 (tmtt) cc_final: 0.9140 (tttp) REVERT: aA 203 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8197 (t80) REVERT: bA 255 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.7875 (t80) REVERT: cA 303 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7307 (t80) REVERT: cA 304 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: dA 355 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7676 (t80) REVERT: eA 403 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8533 (t80) REVERT: eA 404 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8046 (tm-30) REVERT: fA 455 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8102 (t80) REVERT: fA 456 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9123 (tttm) REVERT: mA 56 LYS cc_start: 0.9315 (tttt) cc_final: 0.9062 (tttp) REVERT: oA 156 LYS cc_start: 0.9363 (tmtt) cc_final: 0.9090 (tttp) REVERT: rA 304 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: rA 305 PHE cc_start: 0.8951 (t80) cc_final: 0.8624 (t80) REVERT: sA 355 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7055 (t80) REVERT: sA 356 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8761 (tttm) REVERT: uA 456 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9106 (tttp) REVERT: 1A 56 LYS cc_start: 0.9400 (tmtt) cc_final: 0.9068 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: 4A 205 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8224 (t80) REVERT: 4A 206 LYS cc_start: 0.9208 (tttm) cc_final: 0.8754 (tttm) REVERT: 5A 256 LYS cc_start: 0.9270 (tmtt) cc_final: 0.8896 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9022 (tttm) REVERT: 9A 453 PHE cc_start: 0.8492 (t80) cc_final: 0.8242 (t80) REVERT: 9A 456 LYS cc_start: 0.9160 (tttm) cc_final: 0.8629 (tmtt) REVERT: d 5 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8464 (t80) REVERT: GB 56 LYS cc_start: 0.9350 (tmtt) cc_final: 0.9044 (tmtt) REVERT: JB 205 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8270 (t80) REVERT: KB 256 LYS cc_start: 0.9156 (tmtt) cc_final: 0.8876 (tmtt) REVERT: LB 302 LYS cc_start: 0.9203 (tmtt) cc_final: 0.8894 (ttmm) REVERT: LB 306 LYS cc_start: 0.9367 (tttm) cc_final: 0.9120 (tttm) REVERT: MB 356 LYS cc_start: 0.9086 (tmtt) cc_final: 0.8879 (tmtt) REVERT: VB 52 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8466 (pptt) REVERT: VB 56 LYS cc_start: 0.9436 (tmtt) cc_final: 0.9142 (tptp) REVERT: XB 152 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8519 (pptt) REVERT: XB 157 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7588 (t80) REVERT: YB 205 PHE cc_start: 0.9051 (t80) cc_final: 0.8817 (t80) REVERT: ZB 252 LYS cc_start: 0.9154 (tmtt) cc_final: 0.8500 (pptt) REVERT: aB 304 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: bB 352 LYS cc_start: 0.9133 (tmtt) cc_final: 0.8416 (pptt) REVERT: dB 452 LYS cc_start: 0.9118 (tmtt) cc_final: 0.8347 (pptt) outliers start: 129 outliers final: 74 residues processed: 355 average time/residue: 0.3814 time to fit residues: 161.7977 Evaluate side-chains 442 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 320 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 404 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 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 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 LA residue 306 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 XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS 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 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 sA residue 356 LYS 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=1.00 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.079654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072274 restraints weight = 23440.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.074075 restraints weight = 9048.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.075236 restraints weight = 4629.802| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.6862 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= 2.763 Angle : 2.727 20.718 11300 Z= 1.311 Chirality : 0.138 0.379 800 Planarity : 0.011 0.041 1500 Dihedral : 26.145 89.627 1021 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 117.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.75 % Favored : 74.25 % Rotamer: Outliers : 21.83 % Allowed : 29.33 % Favored : 48.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 0.094 0.011 PHEaA 203 ********************** 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 : 0.879 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: A 6 LYS cc_start: 0.9067 (tttt) cc_final: 0.8715 (tttm) REVERT: A 7 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: K 104 GLU cc_start: 0.8641 (mp0) cc_final: 0.8370 (mp0) REVERT: K 107 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8490 (m-80) REVERT: L 207 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8982 (m-80) REVERT: M 304 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8211 (mp0) REVERT: M 306 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8708 (tttt) REVERT: M 307 PHE cc_start: 0.9458 (OUTLIER) cc_final: 0.8009 (m-10) REVERT: B 4 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8488 (mp0) REVERT: U 404 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7807 (mm-30) REVERT: C 4 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8543 (mp0) REVERT: C 6 LYS cc_start: 0.9188 (tttt) cc_final: 0.8835 (tttm) REVERT: Y 106 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8883 (ttmt) REVERT: k 104 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: E 4 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: E 6 LYS cc_start: 0.9012 (tttt) cc_final: 0.8738 (tttp) REVERT: r 104 GLU cc_start: 0.8716 (mp0) cc_final: 0.8450 (mp0) REVERT: u 404 GLU cc_start: 0.8794 (mp0) cc_final: 0.8545 (mp0) REVERT: u 406 LYS cc_start: 0.9033 (mptt) cc_final: 0.8667 (ttmt) REVERT: F 7 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.8308 (m-10) REVERT: y 104 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: y 107 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: z 206 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8852 (ttpt) REVERT: z 207 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8204 (m-10) REVERT: 0 307 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: G 6 LYS cc_start: 0.9425 (tttt) cc_final: 0.8915 (tttm) REVERT: G 7 PHE cc_start: 0.9336 (OUTLIER) cc_final: 0.7844 (m-10) REVERT: 6 206 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8863 (ttpt) REVERT: 6 207 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8131 (m-10) REVERT: H 4 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: H 6 LYS cc_start: 0.9319 (tttt) cc_final: 0.8864 (tttp) REVERT: EA 302 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8806 (ttmm) REVERT: JA 104 GLU cc_start: 0.4743 (OUTLIER) cc_final: 0.3881 (pm20) REVERT: J 4 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: QA 104 GLU cc_start: 0.8946 (pm20) cc_final: 0.7672 (mm-30) REVERT: SA 304 GLU cc_start: 0.8925 (pm20) cc_final: 0.8421 (mp0) REVERT: TA 404 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8022 (tm-30) REVERT: a 3 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8482 (t80) REVERT: a 4 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8005 (tp30) REVERT: a 6 LYS cc_start: 0.9315 (tttp) cc_final: 0.9094 (tttp) REVERT: XA 52 LYS cc_start: 0.9035 (tmtt) cc_final: 0.8748 (tmtt) REVERT: XA 55 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7829 (t80) REVERT: XA 56 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8954 (tttp) REVERT: YA 104 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8145 (tp30) REVERT: ZA 155 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8096 (t80) REVERT: ZA 156 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9137 (tttp) REVERT: aA 203 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8112 (t80) REVERT: bA 255 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7745 (t80) REVERT: cA 303 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.7285 (t80) REVERT: cA 304 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: dA 355 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7667 (t80) REVERT: eA 403 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8522 (t80) REVERT: eA 404 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8054 (tm-30) REVERT: fA 455 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8091 (t80) REVERT: fA 456 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.9144 (tttm) REVERT: mA 56 LYS cc_start: 0.9314 (tttt) cc_final: 0.9063 (tttp) REVERT: oA 156 LYS cc_start: 0.9369 (tmtt) cc_final: 0.9095 (tttp) REVERT: rA 304 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8202 (tm-30) REVERT: rA 305 PHE cc_start: 0.8945 (t80) cc_final: 0.8625 (t80) REVERT: sA 355 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7066 (t80) REVERT: sA 356 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8779 (tttm) REVERT: uA 456 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9111 (tttp) REVERT: 1A 56 LYS cc_start: 0.9399 (tmtt) cc_final: 0.9070 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8503 (tm-30) REVERT: 4A 205 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8191 (t80) REVERT: 4A 206 LYS cc_start: 0.9219 (tttm) cc_final: 0.8791 (tttm) REVERT: 5A 256 LYS cc_start: 0.9280 (tmtt) cc_final: 0.9012 (tttm) REVERT: 6A 302 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8930 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9038 (tttm) REVERT: 9A 456 LYS cc_start: 0.9155 (tttm) cc_final: 0.8664 (tmtt) REVERT: d 5 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8435 (t80) REVERT: GB 56 LYS cc_start: 0.9347 (tmtt) cc_final: 0.9033 (tmtt) REVERT: JB 205 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8008 (t80) REVERT: KB 256 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8856 (tmtt) REVERT: LB 302 LYS cc_start: 0.9196 (tmtt) cc_final: 0.8893 (ttmm) REVERT: LB 306 LYS cc_start: 0.9426 (tttm) cc_final: 0.9173 (tttm) REVERT: MB 356 LYS cc_start: 0.9085 (tmtt) cc_final: 0.8847 (tmtt) REVERT: VB 52 LYS cc_start: 0.9020 (tmtt) cc_final: 0.8466 (pptt) REVERT: XB 152 LYS cc_start: 0.9070 (tmtt) cc_final: 0.8524 (pptt) REVERT: XB 157 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7586 (t80) REVERT: YB 205 PHE cc_start: 0.9046 (t80) cc_final: 0.8824 (t80) REVERT: ZB 252 LYS cc_start: 0.9159 (tmtt) cc_final: 0.8510 (pptt) REVERT: aB 304 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: bB 352 LYS cc_start: 0.9121 (tmtt) cc_final: 0.8394 (pptt) REVERT: dB 452 LYS cc_start: 0.9123 (tmtt) cc_final: 0.8345 (pptt) outliers start: 131 outliers final: 74 residues processed: 356 average time/residue: 0.3589 time to fit residues: 152.7403 Evaluate side-chains 444 residues out of total 600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 319 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 U residue 404 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 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 LA residue 306 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 XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS 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 sA residue 356 LYS 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 = 0.3416 r_free = 0.3416 target = 0.080117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.072430 restraints weight = 23605.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.074283 restraints weight = 9175.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075491 restraints weight = 4686.699| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.6879 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= 2.763 Angle : 2.734 20.515 11300 Z= 1.313 Chirality : 0.138 0.386 800 Planarity : 0.011 0.041 1500 Dihedral : 26.122 89.637 1021 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 118.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.75 % Favored : 74.25 % Rotamer: Outliers : 22.17 % Allowed : 29.33 % Favored : 48.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (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 0.095 0.011 PHEaA 203 =============================================================================== Job complete usr+sys time: 2768.31 seconds wall clock time: 50 minutes 44.00 seconds (3044.00 seconds total)