Starting phenix.real_space_refine on Wed Sep 17 06:18:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqe_23483/09_2025/7lqe_23483.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqe_23483/09_2025/7lqe_23483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqe_23483/09_2025/7lqe_23483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqe_23483/09_2025/7lqe_23483.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqe_23483/09_2025/7lqe_23483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqe_23483/09_2025/7lqe_23483.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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 4320 2.51 5 N 792 2.21 5 O 936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6048 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "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: "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: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "HA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.50, per 1000 atoms: 0.25 Number of scatterers: 6048 At special positions: 0 Unit cell: (87.48, 77.76, 106.92, 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 936 8.00 N 792 7.00 C 4320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 117.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 7 Processing sheet with id=AA7, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA9, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'h' and resid 2 through 6 removed outlier: 3.535A pdb=" N PHEEA 105 " --> pdb=" O PHE h 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE h 5 " --> pdb=" O PHEEA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 8 105 " --> pdb=" O PHE f 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE f 5 " --> pdb=" O PHE 8 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE 2 105 " --> pdb=" O PHE d 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE d 5 " --> pdb=" O PHE 2 103 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE w 105 " --> pdb=" O PHE b 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE b 5 " --> pdb=" O PHE w 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE t 105 " --> pdb=" O PHE a 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE a 5 " --> pdb=" O PHE t 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE z 105 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE c 5 " --> pdb=" O PHE z 103 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE 5 105 " --> pdb=" O PHE e 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE e 5 " --> pdb=" O PHE 5 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEBA 105 " --> pdb=" O PHE g 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE g 5 " --> pdb=" O PHEBA 103 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHEHA 105 " --> pdb=" O PHE i 3 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE i 5 " --> pdb=" O PHEHA 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'FA' and resid 202 through 206 removed outlier: 3.521A pdb=" N LYSGA 302 " --> pdb=" O GMA 9 208 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS 9 206 " --> pdb=" O GLUGA 304 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GMAGA 308 " --> pdb=" O LYS 9 202 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYSAA 302 " --> pdb=" O GMA 3 208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 3 206 " --> pdb=" O GLUAA 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS 4 302 " --> pdb=" O GMA x 208 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS x 206 " --> pdb=" O GLU 4 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS y 302 " --> pdb=" O GMA u 208 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS u 206 " --> pdb=" O GLU y 304 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GMA y 308 " --> pdb=" O LYS u 202 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS v 302 " --> pdb=" O GMA 0 208 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS 0 206 " --> pdb=" O GLU v 304 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GMA v 308 " --> pdb=" O LYS 0 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS 1 302 " --> pdb=" O GMA 6 208 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS 6 206 " --> pdb=" O GLU 1 304 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 7 302 " --> pdb=" O GMACA 208 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYSCA 206 " --> pdb=" O GLU 7 304 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GMA 7 308 " --> pdb=" O LYSCA 202 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSDA 302 " --> pdb=" O GMAIA 208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYSIA 206 " --> pdb=" O GLUDA 304 " (cutoff:3.500A) 139 hydrogen bonds defined for protein. 393 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: 0.84 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 773 1.26 - 1.33: 667 1.33 - 1.41: 1800 1.41 - 1.48: 651 1.48 - 1.56: 2373 Bond restraints: 6264 Sorted by residual: bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.459 -0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR i 1 " pdb=" CAL 5CR i 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.45e+01 bond pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " ideal model delta sigma weight residual 1.341 1.458 -0.117 2.00e-02 2.50e+03 3.44e+01 ... (remaining 6259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 7119 1.98 - 3.96: 795 3.96 - 5.95: 159 5.95 - 7.93: 54 7.93 - 9.91: 9 Bond angle restraints: 8136 Sorted by residual: angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.82 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" N 5CR h 1 " pdb=" CAL 5CR h 1 " pdb=" CAA 5CR h 1 " ideal model delta sigma weight residual 114.91 124.78 -9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " pdb=" CAA 5CR f 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " pdb=" CAA 5CR b 1 " ideal model delta sigma weight residual 114.91 124.77 -9.86 3.00e+00 1.11e-01 1.08e+01 ... (remaining 8131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 2422 15.26 - 30.52: 395 30.52 - 45.78: 171 45.78 - 61.04: 99 61.04 - 76.30: 9 Dihedral angle restraints: 3096 sinusoidal: 1440 harmonic: 1656 Sorted by residual: dihedral pdb=" CA LYS q 106 " pdb=" CB LYS q 106 " pdb=" CG LYS q 106 " pdb=" CD LYS q 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS Y 106 " pdb=" CB LYS Y 106 " pdb=" CG LYS Y 106 " pdb=" CD LYS Y 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.31 58.69 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CA LYS M 106 " pdb=" CB LYS M 106 " pdb=" CG LYS M 106 " pdb=" CD LYS M 106 " ideal model delta sinusoidal sigma weight residual 60.00 1.32 58.68 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 3093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.017: 191 0.017 - 0.035: 166 0.035 - 0.052: 150 0.052 - 0.070: 53 0.070 - 0.087: 16 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA LYS W 202 " pdb=" N LYS W 202 " pdb=" C LYS W 202 " pdb=" CB LYS W 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.91e-01 chirality pdb=" CA LYS Q 202 " pdb=" N LYS Q 202 " pdb=" C LYS Q 202 " pdb=" CB LYS Q 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.90e-01 chirality pdb=" CA LYS N 202 " pdb=" N LYS N 202 " pdb=" C LYS N 202 " pdb=" CB LYS N 202 " both_signs ideal model delta sigma weight residual False 2.51 2.42 0.09 2.00e-01 2.50e+01 1.87e-01 ... (remaining 573 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE u 205 " -0.009 2.00e-02 2.50e+03 6.94e-03 8.42e-01 pdb=" CG PHE u 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE u 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE u 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE u 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 6 205 " -0.009 2.00e-02 2.50e+03 6.93e-03 8.39e-01 pdb=" CG PHE 6 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE 6 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE 6 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE 6 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE 6 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE x 205 " -0.009 2.00e-02 2.50e+03 6.90e-03 8.33e-01 pdb=" CG PHE x 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE x 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE x 205 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE x 205 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE x 205 " -0.003 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 2593 2.92 - 3.41: 5352 3.41 - 3.91: 9925 3.91 - 4.40: 12294 4.40 - 4.90: 20848 Nonbonded interactions: 51012 Sorted by model distance: nonbonded pdb=" N GLU D 4 " pdb=" OE1 GLU D 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU E 4 " pdb=" OE1 GLU E 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU B 4 " pdb=" OE1 GLU B 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU F 4 " pdb=" OE1 GLU F 4 " model vdw 2.423 3.120 nonbonded pdb=" N GLU A 4 " pdb=" OE1 GLU A 4 " model vdw 2.423 3.120 ... (remaining 51007 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 '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GA' selection = chain 'H' selection = chain 'HA' selection = chain 'I' selection = chain 'IA' selection = chain 'J' selection = chain 'JA' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.118 6264 Z= 0.782 Angle : 1.417 9.910 8136 Z= 0.592 Chirality : 0.035 0.087 576 Planarity : 0.002 0.009 1080 Dihedral : 20.718 76.296 1944 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 14.58 % Allowed : 14.58 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.94 (0.25), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.52 (0.19), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE u 205 Details of bonding type rmsd covalent geometry : bond 0.01603 ( 6264) covalent geometry : angle 1.41685 ( 8136) hydrogen bonds : bond 0.31155 ( 139) hydrogen bonds : angle 15.44596 ( 393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 143 time to evaluate : 0.168 Fit side-chains REVERT: A 2 LYS cc_start: 0.8975 (tttt) cc_final: 0.8577 (tptt) REVERT: J 102 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8362 (mtpt) REVERT: K 202 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8709 (ttmt) REVERT: K 206 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8037 (ttmm) REVERT: L 304 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6841 (mm-30) REVERT: L 306 LYS cc_start: 0.8718 (tttt) cc_final: 0.8208 (mmmm) REVERT: B 2 LYS cc_start: 0.8950 (tttt) cc_final: 0.8747 (tttp) REVERT: M 102 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8316 (ttmm) REVERT: N 202 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8696 (ttmm) REVERT: N 204 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7046 (mt-10) REVERT: O 306 LYS cc_start: 0.8895 (tttt) cc_final: 0.8380 (mmmm) REVERT: C 2 LYS cc_start: 0.8858 (tttt) cc_final: 0.8520 (ttmm) REVERT: P 102 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8714 (ttmt) REVERT: P 104 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6835 (mm-30) REVERT: Q 204 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7270 (mt-10) REVERT: R 304 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6963 (mm-30) REVERT: R 306 LYS cc_start: 0.8731 (tttt) cc_final: 0.8294 (mmmm) REVERT: D 2 LYS cc_start: 0.8945 (tttt) cc_final: 0.8716 (ttmm) REVERT: S 102 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8641 (ttmt) REVERT: U 304 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6582 (mm-30) REVERT: U 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8235 (mmmm) REVERT: E 4 GLU cc_start: 0.7580 (mp0) cc_final: 0.5848 (mp0) REVERT: V 102 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8592 (ttmt) REVERT: V 104 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6989 (mm-30) REVERT: W 202 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8626 (ttmm) REVERT: W 204 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7274 (mt-10) REVERT: W 206 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8144 (ttmm) REVERT: X 304 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7245 (mm-30) REVERT: X 306 LYS cc_start: 0.8889 (tttt) cc_final: 0.8236 (mmmm) REVERT: F 2 LYS cc_start: 0.8964 (tttt) cc_final: 0.8518 (tttm) REVERT: F 4 GLU cc_start: 0.7595 (mp0) cc_final: 0.7012 (mp0) REVERT: Y 102 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8225 (ttpt) REVERT: Z 202 LYS cc_start: 0.8947 (mtpt) cc_final: 0.8683 (ttmm) REVERT: Z 206 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8130 (ttmm) REVERT: j 304 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7285 (mm-30) REVERT: j 306 LYS cc_start: 0.8743 (tttt) cc_final: 0.8240 (mmmm) REVERT: G 2 LYS cc_start: 0.8756 (tttt) cc_final: 0.8452 (tttm) REVERT: G 4 GLU cc_start: 0.7496 (mp0) cc_final: 0.6174 (mp0) REVERT: G 6 LYS cc_start: 0.8210 (mtmt) cc_final: 0.7922 (mtmt) REVERT: k 102 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8561 (mtpt) REVERT: l 202 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8598 (ttmt) REVERT: l 206 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7935 (ttmm) REVERT: m 302 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8498 (mtmt) REVERT: m 304 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7248 (mm-30) REVERT: m 306 LYS cc_start: 0.8693 (tttt) cc_final: 0.8127 (mmmm) REVERT: H 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8810 (ttmt) REVERT: n 102 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8275 (mtpt) REVERT: p 306 LYS cc_start: 0.8809 (tttt) cc_final: 0.8244 (mmmm) REVERT: r 202 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8843 (ttmt) REVERT: s 302 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8303 (mmtt) REVERT: s 306 LYS cc_start: 0.8710 (tttt) cc_final: 0.8340 (tppt) REVERT: a 6 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: w 104 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: z 105 PHE cc_start: 0.8273 (t80) cc_final: 0.7515 (t80) REVERT: 2 105 PHE cc_start: 0.8345 (t80) cc_final: 0.7759 (t80) REVERT: 4 303 PHE cc_start: 0.8424 (t80) cc_final: 0.8200 (t80) REVERT: 4 307 PHE cc_start: 0.7856 (t80) cc_final: 0.7604 (t80) REVERT: HA 104 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7192 (pm20) REVERT: HA 105 PHE cc_start: 0.8203 (t80) cc_final: 0.7558 (t80) REVERT: JA 303 PHE cc_start: 0.8181 (t80) cc_final: 0.7871 (t80) REVERT: JA 307 PHE cc_start: 0.7572 (t80) cc_final: 0.7215 (t80) outliers start: 63 outliers final: 25 residues processed: 178 average time/residue: 0.1736 time to fit residues: 35.4888 Evaluate side-chains 175 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 137 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 102 LYS Chi-restraints excluded: chain J residue 106 LYS Chi-restraints excluded: chain M residue 102 LYS Chi-restraints excluded: chain M residue 106 LYS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain S residue 102 LYS Chi-restraints excluded: chain S residue 106 LYS Chi-restraints excluded: chain V residue 102 LYS Chi-restraints excluded: chain V residue 106 LYS Chi-restraints excluded: chain Y residue 102 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain k residue 102 LYS Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain m residue 302 LYS Chi-restraints excluded: chain n residue 102 LYS Chi-restraints excluded: chain n residue 106 LYS Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 6 LYS Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 104 GLU Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain d residue 2 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain e residue 2 LYS Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 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 = 0.3042 r_free = 0.3042 target = 0.062158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.051987 restraints weight = 19556.897| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.28 r_work: 0.2567 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.7734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.148 0.428 6264 Z= 6.461 Angle : 4.897 39.945 8136 Z= 2.276 Chirality : 0.383 1.034 576 Planarity : 0.025 0.081 1080 Dihedral : 23.687 142.877 861 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 123.74 Ramachandran Plot: Outliers : 3.82 % Allowed : 18.06 % Favored : 78.12 % Rotamer: Outliers : 22.45 % Allowed : 16.67 % Favored : 60.88 % Cbeta Deviations : 38.72 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.97 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.55 (0.30), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.99 (0.23), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.174 0.027 PHE 7 303 Details of bonding type rmsd covalent geometry : bond 0.14792 ( 6264) covalent geometry : angle 4.89711 ( 8136) hydrogen bonds : bond 0.26385 ( 139) hydrogen bonds : angle 13.08566 ( 393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 140 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8721 (mp0) cc_final: 0.8072 (mp0) REVERT: J 104 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7875 (mm-30) REVERT: L 304 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8682 (mm-30) REVERT: M 106 LYS cc_start: 0.9306 (mmmm) cc_final: 0.9054 (mmmm) REVERT: N 204 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8440 (mt-10) REVERT: O 307 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8615 (t80) REVERT: C 2 LYS cc_start: 0.9302 (tttt) cc_final: 0.9087 (tptm) REVERT: C 4 GLU cc_start: 0.8334 (mp0) cc_final: 0.7246 (mp0) REVERT: P 102 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9106 (ttpt) REVERT: P 106 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8863 (mmmm) REVERT: D 2 LYS cc_start: 0.9479 (tttt) cc_final: 0.9278 (ttmm) REVERT: D 4 GLU cc_start: 0.8931 (mp0) cc_final: 0.8094 (mp0) REVERT: S 106 LYS cc_start: 0.9172 (mmmm) cc_final: 0.8827 (mmmm) REVERT: U 306 LYS cc_start: 0.9210 (tttt) cc_final: 0.8919 (ttmm) REVERT: E 4 GLU cc_start: 0.8694 (mp0) cc_final: 0.8132 (mp0) REVERT: E 6 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8887 (mmmt) REVERT: W 205 PHE cc_start: 0.9465 (OUTLIER) cc_final: 0.8767 (m-10) REVERT: X 307 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.8645 (t80) REVERT: F 2 LYS cc_start: 0.9489 (tttt) cc_final: 0.9111 (tttp) REVERT: Y 104 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8525 (mm-30) REVERT: k 104 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8559 (mm-30) REVERT: k 106 LYS cc_start: 0.9275 (mmmm) cc_final: 0.8872 (mmmm) REVERT: m 306 LYS cc_start: 0.9388 (tttt) cc_final: 0.9001 (ttmm) REVERT: H 2 LYS cc_start: 0.9504 (tttt) cc_final: 0.9281 (tttp) REVERT: n 106 LYS cc_start: 0.9133 (tptm) cc_final: 0.8896 (tptm) REVERT: p 306 LYS cc_start: 0.9307 (mttt) cc_final: 0.9097 (mmmm) REVERT: s 302 LYS cc_start: 0.9457 (tttt) cc_final: 0.8893 (tptt) REVERT: s 306 LYS cc_start: 0.9372 (tttt) cc_final: 0.9039 (tptt) REVERT: a 4 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8139 (tp30) REVERT: y 303 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8200 (t80) REVERT: 0 204 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8139 (tm-30) REVERT: d 2 LYS cc_start: 0.9052 (ptpt) cc_final: 0.8758 (ptpt) REVERT: 3 204 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8018 (tm-30) REVERT: 4 302 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8704 (tptp) REVERT: 7 302 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8547 (tptp) REVERT: f 2 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8785 (ttpt) REVERT: f 4 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: 8 102 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8842 (tptm) REVERT: 8 104 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8272 (tm-30) REVERT: BA 107 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8699 (t80) REVERT: DA 306 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8476 (tptp) REVERT: FA 206 LYS cc_start: 0.9108 (tttt) cc_final: 0.8535 (pptt) REVERT: GA 302 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8600 (tptp) REVERT: HA 104 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8454 (pp20) outliers start: 97 outliers final: 56 residues processed: 214 average time/residue: 0.1822 time to fit residues: 44.4357 Evaluate side-chains 210 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 139 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain V residue 106 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain r residue 206 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain t residue 106 LYS Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 102 LYS Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 105 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 8 residue 105 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain HA residue 105 PHE Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.3020 r_free = 0.3020 target = 0.060815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.050802 restraints weight = 19679.050| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.22 r_work: 0.2562 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.8255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.430 6264 Z= 6.498 Angle : 4.912 33.841 8136 Z= 2.286 Chirality : 0.384 1.042 576 Planarity : 0.024 0.088 1080 Dihedral : 23.334 89.858 767 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 129.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 27.78 % Favored : 71.88 % Rotamer: Outliers : 23.15 % Allowed : 26.39 % Favored : 50.46 % Cbeta Deviations : 41.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.92 (0.32), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.27 (0.24), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.189 0.025 PHE 7 303 Details of bonding type rmsd covalent geometry : bond 0.14866 ( 6264) covalent geometry : angle 4.91206 ( 8136) hydrogen bonds : bond 0.26570 ( 139) hydrogen bonds : angle 13.20743 ( 393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 139 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8977 (mtmt) REVERT: J 104 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8251 (mm-30) REVERT: J 107 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.8312 (t80) REVERT: L 304 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8575 (mm-30) REVERT: L 306 LYS cc_start: 0.9344 (mmmm) cc_final: 0.8682 (mmmm) REVERT: L 307 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8844 (m-80) REVERT: M 106 LYS cc_start: 0.9328 (mmmm) cc_final: 0.9103 (mmmm) REVERT: N 204 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8651 (tt0) REVERT: O 307 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8620 (t80) REVERT: C 2 LYS cc_start: 0.9223 (tttt) cc_final: 0.8926 (tttm) REVERT: P 102 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9072 (ttpt) REVERT: P 106 LYS cc_start: 0.9087 (mmmm) cc_final: 0.8821 (mmmm) REVERT: S 106 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8846 (mmmm) REVERT: U 306 LYS cc_start: 0.9186 (tttt) cc_final: 0.8851 (ttmm) REVERT: V 104 GLU cc_start: 0.8942 (mp0) cc_final: 0.8686 (mp0) REVERT: W 205 PHE cc_start: 0.9477 (OUTLIER) cc_final: 0.8815 (m-10) REVERT: X 307 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.8764 (t80) REVERT: F 2 LYS cc_start: 0.9505 (tttt) cc_final: 0.9111 (tttp) REVERT: F 6 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8938 (mmmt) REVERT: Y 102 LYS cc_start: 0.9531 (mtpt) cc_final: 0.9242 (mtmt) REVERT: Z 203 PHE cc_start: 0.9418 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: j 306 LYS cc_start: 0.9341 (mttt) cc_final: 0.9013 (mmmm) REVERT: j 307 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8174 (t80) REVERT: G 4 GLU cc_start: 0.8688 (mp0) cc_final: 0.8398 (mp0) REVERT: k 106 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8906 (mmmm) REVERT: m 306 LYS cc_start: 0.9382 (tttt) cc_final: 0.9065 (mmmm) REVERT: m 307 PHE cc_start: 0.9436 (OUTLIER) cc_final: 0.8967 (t80) REVERT: H 2 LYS cc_start: 0.9485 (tttt) cc_final: 0.9263 (tttp) REVERT: n 106 LYS cc_start: 0.9143 (tptm) cc_final: 0.8891 (tptm) REVERT: o 207 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8671 (t80) REVERT: p 306 LYS cc_start: 0.9380 (mttt) cc_final: 0.9117 (mmmm) REVERT: I 6 LYS cc_start: 0.9251 (mtmt) cc_final: 0.8837 (mtmt) REVERT: q 107 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.8899 (m-80) REVERT: s 302 LYS cc_start: 0.9399 (tttt) cc_final: 0.8825 (tptt) REVERT: s 306 LYS cc_start: 0.9423 (tttt) cc_final: 0.9073 (tptt) REVERT: y 302 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8643 (tptp) REVERT: y 303 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8381 (t80) REVERT: 3 204 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8100 (tm-30) REVERT: f 4 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8058 (tp30) REVERT: BA 103 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8732 (t80) REVERT: BA 107 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.8716 (t80) REVERT: DA 306 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8475 (ptmm) REVERT: h 4 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: GA 302 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8650 (tptp) outliers start: 100 outliers final: 56 residues processed: 213 average time/residue: 0.1830 time to fit residues: 44.6830 Evaluate side-chains 215 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 138 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain R residue 307 PHE Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 4 GLU Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 102 LYS Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.060271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.050339 restraints weight = 19908.836| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.23 r_work: 0.2556 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.8511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.453 6264 Z= 6.514 Angle : 4.937 37.712 8136 Z= 2.296 Chirality : 0.381 0.969 576 Planarity : 0.024 0.086 1080 Dihedral : 23.321 89.619 755 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 130.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 32.29 % Favored : 67.71 % Rotamer: Outliers : 25.23 % Allowed : 28.47 % Favored : 46.30 % Cbeta Deviations : 40.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.32 (0.29), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.57 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.184 0.024 PHE 7 303 Details of bonding type rmsd covalent geometry : bond 0.14908 ( 6264) covalent geometry : angle 4.93687 ( 8136) hydrogen bonds : bond 0.26880 ( 139) hydrogen bonds : angle 13.52013 ( 393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 140 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8602 (mp0) cc_final: 0.8084 (mp0) REVERT: A 6 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8958 (mtmt) REVERT: J 104 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8199 (mm-30) REVERT: L 307 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8976 (m-80) REVERT: M 106 LYS cc_start: 0.9341 (mmmm) cc_final: 0.9111 (mmmm) REVERT: N 204 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8739 (tt0) REVERT: N 205 PHE cc_start: 0.9552 (OUTLIER) cc_final: 0.9285 (m-10) REVERT: O 307 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8633 (t80) REVERT: C 2 LYS cc_start: 0.9262 (tttt) cc_final: 0.8988 (tttm) REVERT: P 102 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9050 (ttpt) REVERT: P 106 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8784 (mmmm) REVERT: R 304 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8169 (mm-30) REVERT: S 106 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8785 (mmmm) REVERT: U 306 LYS cc_start: 0.9184 (tttt) cc_final: 0.8840 (ttmm) REVERT: E 4 GLU cc_start: 0.8521 (mp0) cc_final: 0.8318 (mp0) REVERT: V 104 GLU cc_start: 0.8979 (mp0) cc_final: 0.8708 (mp0) REVERT: W 205 PHE cc_start: 0.9464 (OUTLIER) cc_final: 0.8874 (m-10) REVERT: X 307 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8717 (t80) REVERT: F 2 LYS cc_start: 0.9468 (tttt) cc_final: 0.9063 (tttp) REVERT: F 6 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8981 (mmmt) REVERT: Z 202 LYS cc_start: 0.9430 (OUTLIER) cc_final: 0.9028 (tttt) REVERT: Z 203 PHE cc_start: 0.9426 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: j 307 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8237 (t80) REVERT: k 106 LYS cc_start: 0.9255 (mmmm) cc_final: 0.8904 (mmmm) REVERT: m 306 LYS cc_start: 0.9376 (mttt) cc_final: 0.9082 (mmmm) REVERT: H 2 LYS cc_start: 0.9497 (tttt) cc_final: 0.9276 (tttp) REVERT: n 106 LYS cc_start: 0.9151 (tptm) cc_final: 0.8899 (tptm) REVERT: o 207 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8621 (t80) REVERT: p 303 PHE cc_start: 0.9316 (OUTLIER) cc_final: 0.8683 (m-80) REVERT: I 4 GLU cc_start: 0.8624 (mp0) cc_final: 0.8287 (mp0) REVERT: q 107 PHE cc_start: 0.9456 (OUTLIER) cc_final: 0.8863 (m-80) REVERT: s 302 LYS cc_start: 0.9443 (OUTLIER) cc_final: 0.8797 (tptt) REVERT: s 306 LYS cc_start: 0.9453 (tttt) cc_final: 0.9098 (tppt) REVERT: a 4 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8026 (tp30) REVERT: b 7 PHE cc_start: 0.9568 (OUTLIER) cc_final: 0.9316 (t80) REVERT: y 302 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8570 (tptp) REVERT: y 303 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.8559 (t80) REVERT: 3 204 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8071 (tm-30) REVERT: f 4 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: AA 306 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8567 (tptp) REVERT: BA 107 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8633 (t80) REVERT: DA 306 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8409 (ptmm) REVERT: GA 302 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8697 (tptp) outliers start: 109 outliers final: 68 residues processed: 219 average time/residue: 0.1750 time to fit residues: 44.1458 Evaluate side-chains 234 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 140 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain W residue 206 LYS Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.059994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.050054 restraints weight = 20090.082| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.20 r_work: 0.2561 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.8625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.424 6264 Z= 6.515 Angle : 4.946 36.321 8136 Z= 2.302 Chirality : 0.382 0.959 576 Planarity : 0.024 0.084 1080 Dihedral : 23.421 89.271 752 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 131.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 32.29 % Favored : 67.36 % Rotamer: Outliers : 27.08 % Allowed : 30.09 % Favored : 42.82 % Cbeta Deviations : 41.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.96 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.41 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.64 (0.22), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.024 PHE 7 303 Details of bonding type rmsd covalent geometry : bond 0.14902 ( 6264) covalent geometry : angle 4.94562 ( 8136) hydrogen bonds : bond 0.26934 ( 139) hydrogen bonds : angle 13.57019 ( 393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 142 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8570 (mp0) cc_final: 0.8016 (mp0) REVERT: A 6 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8978 (mtmt) REVERT: J 104 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8202 (mm-30) REVERT: J 107 PHE cc_start: 0.9424 (OUTLIER) cc_final: 0.8473 (t80) REVERT: L 307 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: B 6 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8904 (mtmt) REVERT: M 106 LYS cc_start: 0.9312 (mmmm) cc_final: 0.9088 (mmmm) REVERT: N 205 PHE cc_start: 0.9553 (OUTLIER) cc_final: 0.9241 (m-80) REVERT: O 307 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8624 (t80) REVERT: C 2 LYS cc_start: 0.9226 (tttt) cc_final: 0.8780 (tttm) REVERT: C 6 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8434 (tmmt) REVERT: P 102 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9017 (ttpt) REVERT: P 106 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8771 (mmmm) REVERT: S 106 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8759 (mmmm) REVERT: V 104 GLU cc_start: 0.8935 (mp0) cc_final: 0.8584 (mp0) REVERT: W 205 PHE cc_start: 0.9472 (OUTLIER) cc_final: 0.8965 (m-80) REVERT: X 307 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8708 (t80) REVERT: F 6 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8956 (mmmt) REVERT: Y 106 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8922 (tptm) REVERT: Z 202 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9069 (tttt) REVERT: Z 203 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: Z 204 GLU cc_start: 0.8874 (tt0) cc_final: 0.8670 (tt0) REVERT: j 307 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8310 (t80) REVERT: k 104 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8250 (mm-30) REVERT: k 106 LYS cc_start: 0.9243 (mmmm) cc_final: 0.9036 (mmmm) REVERT: m 306 LYS cc_start: 0.9369 (mttt) cc_final: 0.9139 (mmmm) REVERT: H 2 LYS cc_start: 0.9497 (tttt) cc_final: 0.9275 (tttp) REVERT: n 106 LYS cc_start: 0.9129 (tptm) cc_final: 0.8875 (tptm) REVERT: o 207 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8667 (t80) REVERT: p 303 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8650 (m-80) REVERT: I 4 GLU cc_start: 0.8644 (mp0) cc_final: 0.7671 (mp0) REVERT: q 107 PHE cc_start: 0.9454 (OUTLIER) cc_final: 0.8859 (m-80) REVERT: s 302 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.8791 (tptt) REVERT: s 306 LYS cc_start: 0.9441 (tttt) cc_final: 0.9066 (tppt) REVERT: a 4 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: t 103 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8837 (t80) REVERT: y 302 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8493 (tptp) REVERT: y 303 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8498 (t80) REVERT: d 2 LYS cc_start: 0.9154 (ptpt) cc_final: 0.8891 (ptpt) REVERT: 3 204 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8082 (tm-30) REVERT: 4 303 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8234 (t80) REVERT: e 7 PHE cc_start: 0.9552 (OUTLIER) cc_final: 0.9299 (t80) REVERT: f 4 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: BA 107 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8635 (t80) REVERT: GA 302 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8695 (tptp) outliers start: 117 outliers final: 70 residues processed: 224 average time/residue: 0.1744 time to fit residues: 44.9785 Evaluate side-chains 240 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 142 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 306 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain t residue 103 PHE Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 303 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.2998 r_free = 0.2998 target = 0.059880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.049959 restraints weight = 19876.649| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.21 r_work: 0.2539 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.8694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.425 6264 Z= 6.514 Angle : 4.964 36.434 8136 Z= 2.307 Chirality : 0.383 0.958 576 Planarity : 0.024 0.083 1080 Dihedral : 23.509 89.178 752 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 130.78 Ramachandran Plot: Outliers : 0.35 % Allowed : 31.94 % Favored : 67.71 % Rotamer: Outliers : 27.08 % Allowed : 29.63 % Favored : 43.29 % Cbeta Deviations : 41.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.96 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.44 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.66 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.176 0.024 PHE 7 303 Details of bonding type rmsd covalent geometry : bond 0.14896 ( 6264) covalent geometry : angle 4.96391 ( 8136) hydrogen bonds : bond 0.26936 ( 139) hydrogen bonds : angle 13.64208 ( 393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 141 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8617 (mp0) cc_final: 0.8077 (mp0) REVERT: A 6 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9014 (mtmt) REVERT: J 104 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: J 107 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8440 (t80) REVERT: L 307 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8876 (m-80) REVERT: B 6 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8896 (mtmt) REVERT: M 106 LYS cc_start: 0.9311 (mmmm) cc_final: 0.9087 (mmmm) REVERT: O 307 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8695 (t80) REVERT: C 2 LYS cc_start: 0.9255 (tttt) cc_final: 0.8805 (tttm) REVERT: P 102 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9023 (ttpt) REVERT: P 106 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8775 (mmmm) REVERT: S 106 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8718 (mmmm) REVERT: V 104 GLU cc_start: 0.8985 (mp0) cc_final: 0.8592 (mp0) REVERT: W 205 PHE cc_start: 0.9468 (OUTLIER) cc_final: 0.8967 (m-80) REVERT: X 307 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8704 (t80) REVERT: F 2 LYS cc_start: 0.9467 (tttt) cc_final: 0.9174 (tttp) REVERT: F 6 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8990 (mmmt) REVERT: Y 106 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8918 (tptm) REVERT: Z 202 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9059 (tttt) REVERT: Z 203 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: j 307 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8398 (t80) REVERT: k 104 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8229 (mm-30) REVERT: m 306 LYS cc_start: 0.9365 (mttt) cc_final: 0.9139 (mmmm) REVERT: H 2 LYS cc_start: 0.9488 (tttt) cc_final: 0.9260 (tttp) REVERT: H 4 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.6957 (pm20) REVERT: n 106 LYS cc_start: 0.9123 (tptm) cc_final: 0.8865 (tptm) REVERT: n 107 PHE cc_start: 0.9614 (OUTLIER) cc_final: 0.9397 (m-80) REVERT: o 207 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8652 (t80) REVERT: p 303 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8709 (m-80) REVERT: I 4 GLU cc_start: 0.8681 (mp0) cc_final: 0.7755 (mp0) REVERT: q 107 PHE cc_start: 0.9456 (OUTLIER) cc_final: 0.8863 (m-80) REVERT: s 302 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.8794 (tptt) REVERT: s 306 LYS cc_start: 0.9447 (tttt) cc_final: 0.9117 (tptt) REVERT: a 4 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8026 (tp30) REVERT: b 4 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: y 303 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8721 (t80) REVERT: d 2 LYS cc_start: 0.9154 (ptpt) cc_final: 0.8861 (ptpt) REVERT: 3 204 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8110 (tm-30) REVERT: 4 303 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8059 (t80) REVERT: f 4 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8202 (tp30) REVERT: BA 107 PHE cc_start: 0.9353 (OUTLIER) cc_final: 0.8680 (t80) REVERT: GA 302 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8695 (tptp) outliers start: 117 outliers final: 75 residues processed: 221 average time/residue: 0.1708 time to fit residues: 43.5314 Evaluate side-chains 244 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 141 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 306 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 304 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 0 residue 206 LYS Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain HA residue 104 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.059760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.049889 restraints weight = 19936.264| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.18 r_work: 0.2559 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.8754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.420 6264 Z= 6.517 Angle : 4.967 36.645 8136 Z= 2.307 Chirality : 0.383 0.958 576 Planarity : 0.024 0.084 1080 Dihedral : 23.532 89.073 752 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 131.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.03 % Favored : 65.97 % Rotamer: Outliers : 27.08 % Allowed : 29.86 % Favored : 43.06 % Cbeta Deviations : 42.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.96 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.40 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.64 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.180 0.024 PHE t 103 Details of bonding type rmsd covalent geometry : bond 0.14903 ( 6264) covalent geometry : angle 4.96704 ( 8136) hydrogen bonds : bond 0.26906 ( 139) hydrogen bonds : angle 13.65347 ( 393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 140 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8998 (mtmt) REVERT: J 104 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8158 (mm-30) REVERT: J 107 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.8456 (t80) REVERT: L 307 PHE cc_start: 0.9314 (OUTLIER) cc_final: 0.8887 (m-80) REVERT: B 6 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8906 (mtmt) REVERT: M 106 LYS cc_start: 0.9306 (mmmm) cc_final: 0.9078 (mmmm) REVERT: N 205 PHE cc_start: 0.9543 (OUTLIER) cc_final: 0.9286 (m-10) REVERT: O 303 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8730 (m-10) REVERT: O 307 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.8694 (t80) REVERT: C 2 LYS cc_start: 0.9239 (tttt) cc_final: 0.8762 (tttm) REVERT: P 102 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9024 (ttpt) REVERT: P 106 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8777 (mmmm) REVERT: Q 207 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8433 (t80) REVERT: S 106 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8712 (mmmm) REVERT: V 104 GLU cc_start: 0.8992 (mp0) cc_final: 0.8597 (mp0) REVERT: W 205 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.8951 (m-80) REVERT: X 307 PHE cc_start: 0.9335 (OUTLIER) cc_final: 0.8768 (t80) REVERT: F 2 LYS cc_start: 0.9465 (tttt) cc_final: 0.9163 (tttp) REVERT: F 6 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8986 (mmmt) REVERT: Y 106 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8906 (tptm) REVERT: Z 202 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.9220 (tttt) REVERT: Z 203 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8862 (m-10) REVERT: Z 204 GLU cc_start: 0.8804 (tt0) cc_final: 0.7833 (tm-30) REVERT: j 307 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8383 (t80) REVERT: k 104 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8142 (mm-30) REVERT: k 106 LYS cc_start: 0.9279 (mmmm) cc_final: 0.9029 (mmmm) REVERT: m 306 LYS cc_start: 0.9356 (mttt) cc_final: 0.9128 (mmmm) REVERT: H 4 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: n 106 LYS cc_start: 0.9131 (tptm) cc_final: 0.8872 (tptm) REVERT: n 107 PHE cc_start: 0.9620 (OUTLIER) cc_final: 0.9405 (m-80) REVERT: o 207 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8656 (t80) REVERT: p 303 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8655 (m-80) REVERT: I 4 GLU cc_start: 0.8682 (mp0) cc_final: 0.7790 (mp0) REVERT: q 107 PHE cc_start: 0.9456 (OUTLIER) cc_final: 0.8861 (m-80) REVERT: s 302 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.8796 (tptt) REVERT: s 306 LYS cc_start: 0.9453 (tttt) cc_final: 0.9105 (tptt) REVERT: a 4 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: b 4 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8077 (tp30) REVERT: y 303 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.8738 (t80) REVERT: d 2 LYS cc_start: 0.9149 (ptpt) cc_final: 0.8839 (ptpt) REVERT: 3 204 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8156 (tm-30) REVERT: 4 303 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8007 (t80) REVERT: e 7 PHE cc_start: 0.9568 (OUTLIER) cc_final: 0.9253 (t80) REVERT: f 4 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: BA 107 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8683 (t80) REVERT: GA 302 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8683 (tptp) outliers start: 117 outliers final: 73 residues processed: 221 average time/residue: 0.1722 time to fit residues: 43.9323 Evaluate side-chains 245 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 140 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 306 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain R residue 306 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 202 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 304 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 0 residue 206 LYS Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain e residue 7 PHE Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.059104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.049332 restraints weight = 19608.946| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.16 r_work: 0.2539 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.8791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.421 6264 Z= 6.519 Angle : 4.980 36.475 8136 Z= 2.315 Chirality : 0.383 0.958 576 Planarity : 0.024 0.087 1080 Dihedral : 23.467 89.014 746 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 131.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 31.94 % Favored : 68.06 % Rotamer: Outliers : 27.08 % Allowed : 31.71 % Favored : 41.20 % Cbeta Deviations : 41.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.44 (0.27), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.67 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.187 0.024 PHE t 103 Details of bonding type rmsd covalent geometry : bond 0.14912 ( 6264) covalent geometry : angle 4.97982 ( 8136) hydrogen bonds : bond 0.26897 ( 139) hydrogen bonds : angle 13.69069 ( 393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 139 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.9006 (mtmt) REVERT: J 104 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8160 (mm-30) REVERT: J 107 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8460 (t80) REVERT: L 307 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.8897 (m-80) REVERT: B 6 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8912 (mtmt) REVERT: O 303 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.8779 (m-10) REVERT: O 307 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.8700 (t80) REVERT: C 2 LYS cc_start: 0.9283 (tttt) cc_final: 0.8807 (tttm) REVERT: P 102 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9093 (ttpt) REVERT: P 106 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8804 (mmmm) REVERT: Q 207 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8379 (t80) REVERT: S 106 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8727 (mmmm) REVERT: V 104 GLU cc_start: 0.9012 (mp0) cc_final: 0.8593 (mp0) REVERT: W 205 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.8952 (m-80) REVERT: X 307 PHE cc_start: 0.9352 (OUTLIER) cc_final: 0.8754 (t80) REVERT: F 2 LYS cc_start: 0.9487 (tttt) cc_final: 0.9180 (tttp) REVERT: F 6 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8995 (mmmt) REVERT: Z 203 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.8892 (m-10) REVERT: Z 204 GLU cc_start: 0.8792 (tt0) cc_final: 0.7931 (tm-30) REVERT: j 307 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8429 (t80) REVERT: k 106 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8986 (mmmm) REVERT: m 306 LYS cc_start: 0.9350 (mttt) cc_final: 0.9135 (mmmm) REVERT: H 4 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: H 7 PHE cc_start: 0.9502 (OUTLIER) cc_final: 0.8854 (t80) REVERT: n 106 LYS cc_start: 0.9112 (tptm) cc_final: 0.8876 (tptm) REVERT: n 107 PHE cc_start: 0.9614 (OUTLIER) cc_final: 0.9407 (m-80) REVERT: o 207 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8683 (t80) REVERT: p 303 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8688 (m-80) REVERT: q 107 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.8846 (m-80) REVERT: s 302 LYS cc_start: 0.9444 (OUTLIER) cc_final: 0.8868 (tptt) REVERT: s 306 LYS cc_start: 0.9465 (tttt) cc_final: 0.9170 (tptt) REVERT: a 4 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: b 4 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8188 (tp30) REVERT: y 303 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.8784 (t80) REVERT: d 2 LYS cc_start: 0.9165 (ptpt) cc_final: 0.8871 (ptpt) REVERT: 3 204 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8168 (tm-30) REVERT: 4 303 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8062 (t80) REVERT: f 4 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8232 (tp30) REVERT: BA 107 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8717 (t80) REVERT: CA 206 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8974 (ptmt) REVERT: GA 302 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8708 (tptp) outliers start: 117 outliers final: 76 residues processed: 221 average time/residue: 0.1766 time to fit residues: 45.0622 Evaluate side-chains 245 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 139 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 306 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 304 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 0 residue 206 LYS Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain AA residue 307 PHE Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain CA residue 206 LYS Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.060272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.050300 restraints weight = 19674.958| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.27 r_work: 0.2528 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.8819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.433 6264 Z= 6.519 Angle : 4.980 36.442 8136 Z= 2.312 Chirality : 0.383 0.958 576 Planarity : 0.024 0.084 1080 Dihedral : 23.477 89.231 746 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 131.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 31.94 % Favored : 67.71 % Rotamer: Outliers : 26.39 % Allowed : 33.33 % Favored : 40.28 % Cbeta Deviations : 41.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.42 (0.27), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.65 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.024 PHE t 103 Details of bonding type rmsd covalent geometry : bond 0.14913 ( 6264) covalent geometry : angle 4.97987 ( 8136) hydrogen bonds : bond 0.26896 ( 139) hydrogen bonds : angle 13.70747 ( 393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 140 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 104 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8150 (mm-30) REVERT: J 107 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.8460 (t80) REVERT: L 307 PHE cc_start: 0.9327 (OUTLIER) cc_final: 0.8890 (m-80) REVERT: B 6 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8887 (mtmt) REVERT: N 205 PHE cc_start: 0.9540 (OUTLIER) cc_final: 0.9231 (m-80) REVERT: O 303 PHE cc_start: 0.9431 (OUTLIER) cc_final: 0.8745 (m-10) REVERT: O 307 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8702 (t80) REVERT: C 2 LYS cc_start: 0.9268 (tttt) cc_final: 0.8799 (tttm) REVERT: P 102 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9072 (ttpt) REVERT: P 106 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8802 (mmmm) REVERT: Q 207 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8323 (t80) REVERT: S 106 LYS cc_start: 0.9219 (mmmm) cc_final: 0.8749 (mmmm) REVERT: V 104 GLU cc_start: 0.8985 (mp0) cc_final: 0.8569 (mp0) REVERT: W 204 GLU cc_start: 0.8840 (tt0) cc_final: 0.8038 (tm-30) REVERT: W 205 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8520 (m-80) REVERT: X 307 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8738 (t80) REVERT: F 2 LYS cc_start: 0.9488 (tttt) cc_final: 0.9196 (tttp) REVERT: F 6 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9004 (mmmt) REVERT: Y 106 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8910 (tptm) REVERT: Z 203 PHE cc_start: 0.9421 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: Z 204 GLU cc_start: 0.8816 (tt0) cc_final: 0.7812 (tm-30) REVERT: j 307 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.8405 (t80) REVERT: k 106 LYS cc_start: 0.9255 (mmmm) cc_final: 0.9022 (mmmm) REVERT: m 306 LYS cc_start: 0.9361 (mttt) cc_final: 0.9141 (mmmm) REVERT: H 4 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: H 7 PHE cc_start: 0.9475 (OUTLIER) cc_final: 0.8834 (t80) REVERT: n 106 LYS cc_start: 0.9118 (tptm) cc_final: 0.8875 (tptm) REVERT: n 107 PHE cc_start: 0.9615 (OUTLIER) cc_final: 0.9406 (m-80) REVERT: o 207 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8682 (t80) REVERT: p 303 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: I 4 GLU cc_start: 0.8712 (mp0) cc_final: 0.8311 (mp0) REVERT: I 6 LYS cc_start: 0.9319 (mtmt) cc_final: 0.8991 (mtmt) REVERT: q 107 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.8843 (m-80) REVERT: s 302 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.8844 (tptt) REVERT: s 306 LYS cc_start: 0.9462 (tttt) cc_final: 0.9137 (tptt) REVERT: a 4 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8022 (tp30) REVERT: b 4 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8051 (tp30) REVERT: b 7 PHE cc_start: 0.9590 (OUTLIER) cc_final: 0.9254 (t80) REVERT: y 303 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8793 (t80) REVERT: d 2 LYS cc_start: 0.9174 (ptpt) cc_final: 0.8864 (ptpt) REVERT: 3 204 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8170 (tm-30) REVERT: 4 303 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8044 (t80) REVERT: f 4 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: BA 107 PHE cc_start: 0.9356 (OUTLIER) cc_final: 0.8708 (t80) REVERT: GA 302 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8706 (tptp) REVERT: JA 302 LYS cc_start: 0.9325 (tptp) cc_final: 0.7711 (pttm) outliers start: 114 outliers final: 77 residues processed: 220 average time/residue: 0.1678 time to fit residues: 42.6106 Evaluate side-chains 248 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 140 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 306 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain N residue 205 PHE Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 304 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 0 residue 206 LYS Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.2974 r_free = 0.2974 target = 0.058900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.049230 restraints weight = 19672.206| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.12 r_work: 0.2542 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.8838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.420 6264 Z= 6.525 Angle : 4.974 36.180 8136 Z= 2.311 Chirality : 0.383 0.959 576 Planarity : 0.024 0.084 1080 Dihedral : 23.480 89.136 746 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 133.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 30.90 % Favored : 68.75 % Rotamer: Outliers : 26.16 % Allowed : 34.03 % Favored : 39.81 % Cbeta Deviations : 42.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.45 (0.27), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.68 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.024 PHE t 103 Details of bonding type rmsd covalent geometry : bond 0.14926 ( 6264) covalent geometry : angle 4.97420 ( 8136) hydrogen bonds : bond 0.26848 ( 139) hydrogen bonds : angle 13.70520 ( 393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 576 Ramachandran restraints generated. 288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 139 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8929 (mtmt) REVERT: J 104 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8163 (mm-30) REVERT: J 107 PHE cc_start: 0.9440 (OUTLIER) cc_final: 0.8460 (t80) REVERT: L 307 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8897 (m-80) REVERT: B 6 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8920 (mtmt) REVERT: O 303 PHE cc_start: 0.9441 (OUTLIER) cc_final: 0.8762 (m-10) REVERT: O 307 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8699 (t80) REVERT: C 2 LYS cc_start: 0.9282 (tttt) cc_final: 0.8809 (tttm) REVERT: P 102 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9090 (ttpt) REVERT: P 106 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8813 (mmmm) REVERT: Q 207 PHE cc_start: 0.9348 (OUTLIER) cc_final: 0.8321 (t80) REVERT: S 106 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8765 (mmmm) REVERT: V 104 GLU cc_start: 0.8984 (mp0) cc_final: 0.8603 (mp0) REVERT: W 204 GLU cc_start: 0.9007 (tt0) cc_final: 0.7890 (tm-30) REVERT: W 205 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.8547 (m-10) REVERT: X 307 PHE cc_start: 0.9347 (OUTLIER) cc_final: 0.8739 (t80) REVERT: F 2 LYS cc_start: 0.9493 (tttt) cc_final: 0.9204 (tttp) REVERT: F 6 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9014 (mmmt) REVERT: Y 106 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8923 (tptm) REVERT: Z 203 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.8976 (m-80) REVERT: Z 204 GLU cc_start: 0.8769 (tt0) cc_final: 0.7764 (tm-30) REVERT: j 307 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8425 (t80) REVERT: k 106 LYS cc_start: 0.9242 (mmmm) cc_final: 0.9026 (mmmm) REVERT: m 306 LYS cc_start: 0.9346 (mttt) cc_final: 0.9128 (mmmm) REVERT: H 4 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: H 7 PHE cc_start: 0.9474 (OUTLIER) cc_final: 0.8838 (t80) REVERT: n 106 LYS cc_start: 0.9114 (tptm) cc_final: 0.8878 (tptm) REVERT: n 107 PHE cc_start: 0.9614 (OUTLIER) cc_final: 0.9411 (m-80) REVERT: o 207 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8681 (t80) REVERT: p 303 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8704 (m-80) REVERT: I 4 GLU cc_start: 0.8659 (mp0) cc_final: 0.8184 (mp0) REVERT: I 6 LYS cc_start: 0.9320 (mtmt) cc_final: 0.9002 (mtmt) REVERT: q 107 PHE cc_start: 0.9444 (OUTLIER) cc_final: 0.8840 (m-80) REVERT: s 302 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.8869 (tptt) REVERT: s 306 LYS cc_start: 0.9460 (tttt) cc_final: 0.9163 (tptt) REVERT: a 4 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8030 (tp30) REVERT: b 4 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: b 7 PHE cc_start: 0.9594 (OUTLIER) cc_final: 0.9301 (t80) REVERT: y 303 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8811 (t80) REVERT: d 2 LYS cc_start: 0.9177 (ptpt) cc_final: 0.8872 (ptpt) REVERT: 3 204 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8171 (tm-30) REVERT: 4 303 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8034 (t80) REVERT: f 4 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8243 (tp30) REVERT: f 5 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.7750 (t80) REVERT: BA 107 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8721 (t80) REVERT: DA 306 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8461 (ptmm) REVERT: GA 302 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8710 (tptp) REVERT: JA 302 LYS cc_start: 0.9300 (tptp) cc_final: 0.7685 (pttm) outliers start: 113 outliers final: 76 residues processed: 218 average time/residue: 0.1719 time to fit residues: 43.2860 Evaluate side-chains 248 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 139 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LYS Chi-restraints excluded: chain J residue 104 GLU Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain L residue 306 LYS Chi-restraints excluded: chain L residue 307 PHE Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain N residue 202 LYS Chi-restraints excluded: chain O residue 303 PHE Chi-restraints excluded: chain O residue 307 PHE Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 207 PHE Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain U residue 306 LYS Chi-restraints excluded: chain U residue 307 PHE Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain W residue 205 PHE Chi-restraints excluded: chain X residue 307 PHE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain Y residue 106 LYS Chi-restraints excluded: chain Z residue 203 PHE Chi-restraints excluded: chain j residue 304 GLU Chi-restraints excluded: chain j residue 307 PHE Chi-restraints excluded: chain m residue 307 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain n residue 107 PHE Chi-restraints excluded: chain o residue 206 LYS Chi-restraints excluded: chain o residue 207 PHE Chi-restraints excluded: chain p residue 303 PHE Chi-restraints excluded: chain q residue 102 LYS Chi-restraints excluded: chain q residue 106 LYS Chi-restraints excluded: chain q residue 107 PHE Chi-restraints excluded: chain s residue 302 LYS Chi-restraints excluded: chain s residue 307 PHE Chi-restraints excluded: chain a residue 2 LYS Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain v residue 302 LYS Chi-restraints excluded: chain v residue 303 PHE Chi-restraints excluded: chain v residue 305 PHE Chi-restraints excluded: chain v residue 307 PHE Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 7 PHE Chi-restraints excluded: chain w residue 102 LYS Chi-restraints excluded: chain w residue 103 PHE Chi-restraints excluded: chain w residue 105 PHE Chi-restraints excluded: chain w residue 106 LYS Chi-restraints excluded: chain y residue 302 LYS Chi-restraints excluded: chain y residue 303 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain z residue 102 LYS Chi-restraints excluded: chain z residue 103 PHE Chi-restraints excluded: chain z residue 105 PHE Chi-restraints excluded: chain 0 residue 206 LYS Chi-restraints excluded: chain 1 residue 302 LYS Chi-restraints excluded: chain 1 residue 303 PHE Chi-restraints excluded: chain 1 residue 305 PHE Chi-restraints excluded: chain 1 residue 306 LYS Chi-restraints excluded: chain d residue 4 GLU Chi-restraints excluded: chain 2 residue 103 PHE Chi-restraints excluded: chain 4 residue 302 LYS Chi-restraints excluded: chain 4 residue 303 PHE Chi-restraints excluded: chain 4 residue 305 PHE Chi-restraints excluded: chain 4 residue 307 PHE Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 4 GLU Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 5 residue 106 LYS Chi-restraints excluded: chain 5 residue 107 PHE Chi-restraints excluded: chain 6 residue 203 PHE Chi-restraints excluded: chain 7 residue 302 LYS Chi-restraints excluded: chain 7 residue 303 PHE Chi-restraints excluded: chain 7 residue 305 PHE Chi-restraints excluded: chain f residue 2 LYS Chi-restraints excluded: chain f residue 4 GLU Chi-restraints excluded: chain f residue 5 PHE Chi-restraints excluded: chain 8 residue 102 LYS Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 206 LYS Chi-restraints excluded: chain AA residue 305 PHE Chi-restraints excluded: chain AA residue 306 LYS Chi-restraints excluded: chain g residue 2 LYS Chi-restraints excluded: chain g residue 3 PHE Chi-restraints excluded: chain g residue 5 PHE Chi-restraints excluded: chain BA residue 103 PHE Chi-restraints excluded: chain BA residue 105 PHE Chi-restraints excluded: chain BA residue 107 PHE Chi-restraints excluded: chain DA residue 303 PHE Chi-restraints excluded: chain DA residue 305 PHE Chi-restraints excluded: chain DA residue 306 LYS Chi-restraints excluded: chain DA residue 307 PHE Chi-restraints excluded: chain h residue 4 GLU Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain EA residue 102 LYS Chi-restraints excluded: chain EA residue 103 PHE Chi-restraints excluded: chain EA residue 105 PHE Chi-restraints excluded: chain EA residue 107 PHE Chi-restraints excluded: chain GA residue 302 LYS Chi-restraints excluded: chain GA residue 303 PHE Chi-restraints excluded: chain GA residue 305 PHE Chi-restraints excluded: chain GA residue 306 LYS Chi-restraints excluded: chain i residue 2 LYS Chi-restraints excluded: chain i residue 3 PHE Chi-restraints excluded: chain i residue 4 GLU Chi-restraints excluded: chain JA residue 303 PHE Chi-restraints excluded: chain JA residue 305 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 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 = 0.2973 r_free = 0.2973 target = 0.058855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.049160 restraints weight = 19705.381| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.15 r_work: 0.2553 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.8849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.149 0.419 6264 Z= 6.521 Angle : 4.976 36.056 8136 Z= 2.312 Chirality : 0.383 0.958 576 Planarity : 0.024 0.084 1080 Dihedral : 23.477 89.062 746 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 133.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 31.60 % Favored : 68.06 % Rotamer: Outliers : 25.69 % Allowed : 34.03 % Favored : 40.28 % Cbeta Deviations : 41.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -7.42 (0.28), residues: 288 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.65 (0.21), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.178 0.024 PHE t 103 Details of bonding type rmsd covalent geometry : bond 0.14914 ( 6264) covalent geometry : angle 4.97616 ( 8136) hydrogen bonds : bond 0.26837 ( 139) hydrogen bonds : angle 13.71092 ( 393) =============================================================================== Job complete usr+sys time: 1397.93 seconds wall clock time: 25 minutes 3.47 seconds (1503.47 seconds total)