Starting phenix.real_space_refine on Tue Sep 24 16:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/09_2024/7lqi_23487.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/09_2024/7lqi_23487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/09_2024/7lqi_23487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/09_2024/7lqi_23487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/09_2024/7lqi_23487.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqi_23487/09_2024/7lqi_23487.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 6000 2.51 5 N 1100 2.21 5 O 1300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 215 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8400 Number of models: 1 Model: "" Number of chains: 100 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "f" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "n" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "t" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "CA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "DA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "EA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "FA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "QA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "RA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "SA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "TA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "XA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "aA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "cA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "dA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "eA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "fA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "mA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "nA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "oA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "pA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "qA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "rA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "sA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "tA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "uA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "1A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "2A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "3A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "6A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "7A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "8A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "9A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "GB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "HB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "IB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "JB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "KB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "LB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "MB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "NB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "OB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "VB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "WB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "XB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "YB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "ZB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "aB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "bB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "cB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "dB" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.42, per 1000 atoms: 0.65 Number of scatterers: 8400 At special positions: 0 Unit cell: (98.28, 98.28, 64.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1300 8.00 N 1100 7.00 C 6000 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 590.4 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'I' and resid 6 through 7 removed outlier: 6.912A pdb=" N LYS G 6 " --> pdb=" O PHE I 7 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS E 6 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS C 6 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS A 6 " --> pdb=" O PHE C 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'JA' and resid 102 through 104 removed outlier: 5.642A pdb=" N LYS K 102 " --> pdb=" O PHE Y 103 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE Y 105 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU K 104 " --> pdb=" O PHE Y 105 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE Y 107 " --> pdb=" O GLU K 104 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS K 106 " --> pdb=" O PHE Y 107 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE K 103 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE R 103 " --> pdb=" O GLU k 104 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE k 103 " --> pdb=" O GLU y 104 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE y 103 " --> pdb=" O GLUCA 104 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYSCA 106 " --> pdb=" O PHE y 103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLUQA 104 " --> pdb=" O PHECA 103 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYSQA 106 " --> pdb=" O PHECA 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'KA' and resid 206 through 207 removed outlier: 7.773A pdb=" N PHEKA 207 " --> pdb=" O GLU 6 204 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS 6 206 " --> pdb=" O PHEKA 207 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS s 202 " --> pdb=" O PHE 6 203 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE 6 205 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU s 204 " --> pdb=" O PHE 6 205 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE 6 207 " --> pdb=" O GLU s 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS s 206 " --> pdb=" O PHE 6 207 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS L 202 " --> pdb=" O PHE Z 203 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE Z 205 " --> pdb=" O LYS L 202 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU L 204 " --> pdb=" O PHE Z 205 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE Z 207 " --> pdb=" O GLU L 204 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS L 206 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE L 203 " --> pdb=" O GLU S 204 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS S 206 " --> pdb=" O PHE L 203 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE L 205 " --> pdb=" O LYS S 206 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE z 203 " --> pdb=" O GLUDA 204 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LYSDA 206 " --> pdb=" O PHE z 203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLURA 204 " --> pdb=" O PHEDA 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYSRA 206 " --> pdb=" O PHEDA 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'KA' and resid 206 through 207 removed outlier: 7.773A pdb=" N PHEKA 207 " --> pdb=" O GLU 6 204 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS 6 206 " --> pdb=" O PHEKA 207 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS s 202 " --> pdb=" O PHE 6 203 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE 6 205 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU s 204 " --> pdb=" O PHE 6 205 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE 6 207 " --> pdb=" O GLU s 204 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS s 206 " --> pdb=" O PHE 6 207 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS L 202 " --> pdb=" O PHE Z 203 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE Z 205 " --> pdb=" O LYS L 202 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU L 204 " --> pdb=" O PHE Z 205 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE Z 207 " --> pdb=" O GLU L 204 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS L 206 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE L 203 " --> pdb=" O GLU S 204 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS S 206 " --> pdb=" O PHE L 203 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE L 205 " --> pdb=" O LYS S 206 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLURA 204 " --> pdb=" O PHEDA 203 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYSRA 206 " --> pdb=" O PHEDA 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LA' and resid 302 through 307 removed outlier: 6.205A pdb=" N LYS 7 302 " --> pdb=" O PHELA 303 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHELA 305 " --> pdb=" O LYS 7 302 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU 7 304 " --> pdb=" O PHELA 305 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHELA 307 " --> pdb=" O GLU 7 304 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS 7 306 " --> pdb=" O PHELA 307 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS t 302 " --> pdb=" O PHE 7 303 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE 7 305 " --> pdb=" O LYS t 302 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU t 304 " --> pdb=" O PHE 7 305 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N PHE 7 307 " --> pdb=" O GLU t 304 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS t 306 " --> pdb=" O PHE 7 307 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LYS M 302 " --> pdb=" O PHE f 303 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE f 305 " --> pdb=" O LYS M 302 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU M 304 " --> pdb=" O PHE f 305 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE f 307 " --> pdb=" O GLU M 304 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS M 306 " --> pdb=" O PHE f 307 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE M 303 " --> pdb=" O GLU T 304 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LYS T 306 " --> pdb=" O PHE M 303 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE M 305 " --> pdb=" O LYS T 306 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE 0 303 " --> pdb=" O GLUEA 304 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LYSEA 306 " --> pdb=" O PHE 0 303 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N PHE 0 305 " --> pdb=" O LYSEA 306 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHEEA 303 " --> pdb=" O GLUSA 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'MA' and resid 402 through 403 removed outlier: 6.357A pdb=" N LYS 8 402 " --> pdb=" O PHEMA 403 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS u 402 " --> pdb=" O PHE 8 403 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS g 402 " --> pdb=" O PHE u 403 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS N 402 " --> pdb=" O PHE g 403 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'MA' and resid 406 through 407 removed outlier: 6.747A pdb=" N LYS 8 406 " --> pdb=" O PHEMA 407 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS u 406 " --> pdb=" O PHE 8 407 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS g 406 " --> pdb=" O PHE u 407 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS N 406 " --> pdb=" O PHE g 407 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3 removed outlier: 6.791A pdb=" N LYS C 2 " --> pdb=" O PHE E 3 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS E 2 " --> pdb=" O PHE G 3 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS G 2 " --> pdb=" O PHE I 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'd' and resid 5 through 6 removed outlier: 3.743A pdb=" N LYS b 6 " --> pdb=" O GLUGB 54 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS a 6 " --> pdb=" O GLUmA 54 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS c 6 " --> pdb=" O GLUXA 54 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSXA 56 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE1A 55 " --> pdb=" O PHE c 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS e 6 " --> pdb=" O GLU1A 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'HB' and resid 105 through 106 removed outlier: 3.686A pdb=" N LYSnA 106 " --> pdb=" O GLUIB 154 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYSYA 106 " --> pdb=" O GLUoA 154 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS2A 106 " --> pdb=" O GLUZA 154 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYSWB 106 " --> pdb=" O GLU3A 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'JB' and resid 205 through 206 removed outlier: 3.810A pdb=" N PHEKB 253 " --> pdb=" O PHEJB 205 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSpA 206 " --> pdb=" O GLUKB 254 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYSKB 256 " --> pdb=" O GLUpA 204 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHEqA 255 " --> pdb=" O PHEpA 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHEqA 253 " --> pdb=" O PHEpA 205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYSqA 256 " --> pdb=" O GLUaA 204 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHEbA 255 " --> pdb=" O PHEaA 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHEbA 253 " --> pdb=" O PHEaA 205 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYSbA 256 " --> pdb=" O GLU4A 204 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE5A 255 " --> pdb=" O PHE4A 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE5A 253 " --> pdb=" O PHE4A 205 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYSYB 206 " --> pdb=" O GLU5A 254 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS5A 256 " --> pdb=" O GLUYB 204 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHEZB 253 " --> pdb=" O PHEYB 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LB' and resid 305 through 306 removed outlier: 3.555A pdb=" N PHEMB 353 " --> pdb=" O PHELB 305 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYSrA 306 " --> pdb=" O GLUMB 354 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSMB 356 " --> pdb=" O GLUrA 304 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHEsA 355 " --> pdb=" O PHErA 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHEsA 353 " --> pdb=" O PHErA 305 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYScA 306 " --> pdb=" O GLUsA 354 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHEdA 355 " --> pdb=" O PHEcA 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHEdA 353 " --> pdb=" O PHEcA 305 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS6A 306 " --> pdb=" O GLUdA 354 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE7A 355 " --> pdb=" O PHE6A 303 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE7A 353 " --> pdb=" O PHE6A 305 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU7A 354 " --> pdb=" O LYSaB 306 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYSaB 306 " --> pdb=" O GLU7A 354 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHEbB 353 " --> pdb=" O PHEaB 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'NB' and resid 405 through 406 removed outlier: 3.651A pdb=" N LYStA 406 " --> pdb=" O GLUOB 454 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYSeA 406 " --> pdb=" O GLUuA 454 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS8A 406 " --> pdb=" O GLUfA 454 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYScB 406 " --> pdb=" O GLU9A 454 " (cutoff:3.500A) 152 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.25: 994 1.25 - 1.33: 736 1.33 - 1.40: 2770 1.40 - 1.47: 900 1.47 - 1.54: 3300 Bond restraints: 8700 Sorted by residual: bond pdb=" N 5CRpA 201 " pdb=" CAL 5CRpA 201 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N 5CRaA 201 " pdb=" CAL 5CRaA 201 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N 5CRHB 101 " pdb=" CAL 5CRHB 101 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" N 5CR8A 401 " pdb=" CAL 5CR8A 401 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" N 5CRnA 101 " pdb=" CAL 5CRnA 101 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.12e+01 ... (remaining 8695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 9967 1.87 - 3.74: 949 3.74 - 5.61: 295 5.61 - 7.48: 20 7.48 - 9.35: 69 Bond angle restraints: 11300 Sorted by residual: angle pdb=" CA 5CR U 401 " pdb=" N 5CR U 401 " pdb=" CAL 5CR U 401 " ideal model delta sigma weight residual 125.23 115.88 9.35 3.00e+00 1.11e-01 9.70e+00 angle pdb=" CA 5CR u 401 " pdb=" N 5CR u 401 " pdb=" CAL 5CR u 401 " ideal model delta sigma weight residual 125.23 115.89 9.34 3.00e+00 1.11e-01 9.69e+00 angle pdb=" CA 5CR n 401 " pdb=" N 5CR n 401 " pdb=" CAL 5CR n 401 " ideal model delta sigma weight residual 125.23 115.90 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA 5CRFA 401 " pdb=" N 5CRFA 401 " pdb=" CAL 5CRFA 401 " ideal model delta sigma weight residual 125.23 115.90 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" CA 5CRMA 401 " pdb=" N 5CRMA 401 " pdb=" CAL 5CRMA 401 " ideal model delta sigma weight residual 125.23 115.90 9.33 3.00e+00 1.11e-01 9.67e+00 ... (remaining 11295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 3570 16.29 - 32.58: 425 32.58 - 48.87: 145 48.87 - 65.15: 125 65.15 - 81.44: 35 Dihedral angle restraints: 4300 sinusoidal: 2000 harmonic: 2300 Sorted by residual: dihedral pdb=" CA PHEaA 205 " pdb=" C PHEaA 205 " pdb=" N LYSaA 206 " pdb=" CA LYSaA 206 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHEJB 205 " pdb=" C PHEJB 205 " pdb=" N LYSJB 206 " pdb=" CA LYSJB 206 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA PHEYB 205 " pdb=" C PHEYB 205 " pdb=" N LYSYB 206 " pdb=" CA LYSYB 206 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 4297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.014: 229 0.014 - 0.029: 321 0.029 - 0.043: 198 0.043 - 0.057: 42 0.057 - 0.072: 10 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA GLU 1 404 " pdb=" N GLU 1 404 " pdb=" C GLU 1 404 " pdb=" CB GLU 1 404 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.28e-01 chirality pdb=" CA GLU n 404 " pdb=" N GLU n 404 " pdb=" C GLU n 404 " pdb=" CB GLU n 404 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.25e-01 chirality pdb=" CA GLU N 404 " pdb=" N GLU N 404 " pdb=" C GLU N 404 " pdb=" CB GLU N 404 " both_signs ideal model delta sigma weight residual False 2.51 2.58 -0.07 2.00e-01 2.50e+01 1.21e-01 ... (remaining 797 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEpA 205 " -0.007 2.00e-02 2.50e+03 7.22e-03 9.11e-01 pdb=" CG PHEpA 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEpA 205 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEpA 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEpA 205 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHEpA 205 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHEpA 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEJB 205 " -0.007 2.00e-02 2.50e+03 7.08e-03 8.78e-01 pdb=" CG PHEJB 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHEJB 205 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEJB 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEJB 205 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHEJB 205 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHEJB 205 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE4A 205 " -0.007 2.00e-02 2.50e+03 7.05e-03 8.71e-01 pdb=" CG PHE4A 205 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE4A 205 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE4A 205 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE4A 205 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE4A 205 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE4A 205 " -0.002 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2545 2.77 - 3.31: 6509 3.31 - 3.84: 13602 3.84 - 4.37: 17423 4.37 - 4.90: 28904 Nonbonded interactions: 68983 Sorted by model distance: nonbonded pdb=" OE1 GMAcB 408 " pdb=" N2 GMAcB 408 " model vdw 2.242 3.120 nonbonded pdb=" OE1 GMAeA 408 " pdb=" N2 GMAeA 408 " model vdw 2.242 3.120 nonbonded pdb=" OE1 GMAtA 408 " pdb=" N2 GMAtA 408 " model vdw 2.243 3.120 nonbonded pdb=" OE1 GMANB 408 " pdb=" N2 GMANB 408 " model vdw 2.243 3.120 nonbonded pdb=" OE1 GMA8A 408 " pdb=" N2 GMA8A 408 " model vdw 2.243 3.120 ... (remaining 68978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '1A' selection = chain '2A' selection = chain '3A' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '6A' selection = chain '7' selection = chain '7A' selection = chain '8' selection = chain '8A' selection = chain '9A' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'CA' selection = chain 'D' selection = chain 'DA' selection = chain 'E' selection = chain 'EA' selection = chain 'F' selection = chain 'FA' selection = chain 'G' selection = chain 'GB' selection = chain 'H' selection = chain 'HB' selection = chain 'I' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'NB' selection = chain 'OB' selection = chain 'QA' selection = chain 'R' selection = chain 'RA' selection = chain 'S' selection = chain 'SA' selection = chain 'T' selection = chain 'TA' selection = chain 'U' selection = chain 'VB' selection = chain 'WB' selection = chain 'XA' selection = chain 'XB' selection = chain 'Y' selection = chain 'YA' selection = chain 'YB' selection = chain 'Z' selection = chain 'ZA' selection = chain 'ZB' selection = chain 'a' selection = chain 'aA' selection = chain 'aB' selection = chain 'b' selection = chain 'bA' selection = chain 'bB' selection = chain 'c' selection = chain 'cA' selection = chain 'cB' selection = chain 'd' selection = chain 'dA' selection = chain 'dB' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'oA' selection = chain 'pA' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.010 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: 0.130 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.380 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.112 8700 Z= 0.861 Angle : 1.399 9.345 11300 Z= 0.568 Chirality : 0.027 0.072 800 Planarity : 0.002 0.007 1500 Dihedral : 20.423 81.443 2700 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.00 % Allowed : 8.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHEpA 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 368 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 302 LYS cc_start: 0.8276 (tttt) cc_final: 0.7660 (tttm) REVERT: N 404 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6945 (mm-30) REVERT: B 2 LYS cc_start: 0.8999 (tttt) cc_final: 0.8790 (ttmm) REVERT: B 4 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: S 202 LYS cc_start: 0.9090 (tttt) cc_final: 0.8886 (ttmt) REVERT: U 402 LYS cc_start: 0.9254 (tttt) cc_final: 0.9045 (ttmm) REVERT: U 404 GLU cc_start: 0.7725 (mm-30) cc_final: 0.6851 (mt-10) REVERT: C 2 LYS cc_start: 0.8944 (tttt) cc_final: 0.8666 (tttm) REVERT: C 4 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7793 (mm-30) REVERT: C 6 LYS cc_start: 0.8693 (tttt) cc_final: 0.8425 (tttp) REVERT: g 406 LYS cc_start: 0.8843 (ttmt) cc_final: 0.8330 (tttp) REVERT: l 204 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: m 302 LYS cc_start: 0.9180 (tttt) cc_final: 0.8905 (ttmt) REVERT: E 4 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7672 (tm-30) REVERT: t 302 LYS cc_start: 0.9052 (tttt) cc_final: 0.8815 (ttmm) REVERT: u 402 LYS cc_start: 0.9187 (tttt) cc_final: 0.8774 (ttmm) REVERT: F 2 LYS cc_start: 0.9203 (tttt) cc_final: 0.8897 (tttm) REVERT: y 106 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8723 (tttm) REVERT: 0 304 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7420 (mt-10) REVERT: 1 406 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8652 (ttpt) REVERT: 5 104 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8142 (tm-30) REVERT: 6 204 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: 8 402 LYS cc_start: 0.9116 (tttt) cc_final: 0.8904 (tttp) REVERT: 8 404 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7144 (mt-10) REVERT: H 6 LYS cc_start: 0.8646 (tttt) cc_final: 0.8276 (tptt) REVERT: I 4 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6426 (pm20) REVERT: XA 53 PHE cc_start: 0.7733 (t80) cc_final: 0.7514 (t80) REVERT: XA 56 LYS cc_start: 0.8832 (tmtt) cc_final: 0.8355 (tmtt) REVERT: YA 105 PHE cc_start: 0.8199 (t80) cc_final: 0.7996 (t80) REVERT: ZA 156 LYS cc_start: 0.8788 (tmtt) cc_final: 0.8462 (tmtt) REVERT: aA 206 LYS cc_start: 0.9027 (tttm) cc_final: 0.8764 (tttp) REVERT: bA 257 PHE cc_start: 0.7440 (t80) cc_final: 0.7230 (t80) REVERT: cA 302 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8056 (tmtt) REVERT: dA 352 LYS cc_start: 0.8915 (tmtt) cc_final: 0.8684 (tmtt) REVERT: eA 406 LYS cc_start: 0.9333 (tttp) cc_final: 0.9115 (tttp) REVERT: fA 456 LYS cc_start: 0.8801 (tmtt) cc_final: 0.8472 (tmtt) REVERT: mA 56 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8438 (tptp) REVERT: oA 154 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8011 (tm-30) REVERT: oA 156 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8418 (tptp) REVERT: qA 254 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8044 (tm-30) REVERT: rA 302 LYS cc_start: 0.8806 (tmtt) cc_final: 0.8484 (tmtt) REVERT: sA 354 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8060 (tm-30) REVERT: sA 356 LYS cc_start: 0.8669 (tmtt) cc_final: 0.8441 (tmtt) REVERT: tA 406 LYS cc_start: 0.9404 (tttp) cc_final: 0.9192 (tttm) REVERT: uA 456 LYS cc_start: 0.8623 (tmtt) cc_final: 0.8334 (tmtt) REVERT: 3A 152 LYS cc_start: 0.8829 (tmtt) cc_final: 0.8615 (tmtt) REVERT: 5A 256 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8288 (tmtt) REVERT: 7A 352 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8611 (tmtt) REVERT: 7A 356 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8294 (tmtt) REVERT: GB 52 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8658 (tmtt) REVERT: GB 56 LYS cc_start: 0.8880 (tmtt) cc_final: 0.8650 (tmtt) REVERT: HB 107 PHE cc_start: 0.9122 (t80) cc_final: 0.8172 (t80) REVERT: JB 207 PHE cc_start: 0.9068 (t80) cc_final: 0.8360 (t80) REVERT: KB 256 LYS cc_start: 0.8718 (tmtt) cc_final: 0.8484 (tmtt) REVERT: LB 302 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8360 (ttmm) REVERT: LB 305 PHE cc_start: 0.8372 (t80) cc_final: 0.8169 (t80) REVERT: MB 353 PHE cc_start: 0.7755 (t80) cc_final: 0.7514 (t80) REVERT: MB 356 LYS cc_start: 0.8703 (tmtt) cc_final: 0.8472 (tmtt) REVERT: OB 452 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8586 (tmtt) REVERT: OB 456 LYS cc_start: 0.8888 (tmtt) cc_final: 0.8582 (tmtt) REVERT: ZB 256 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8675 (tmtt) outliers start: 30 outliers final: 4 residues processed: 373 average time/residue: 0.4025 time to fit residues: 176.7239 Evaluate side-chains 340 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 330 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain z residue 204 GLU Chi-restraints excluded: chain 6 residue 204 GLU Chi-restraints excluded: chain I residue 4 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.224 8700 Z= 2.767 Angle : 2.721 17.844 11300 Z= 1.297 Chirality : 0.136 0.319 800 Planarity : 0.012 0.039 1500 Dihedral : 26.959 89.476 1030 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 115.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.00 % Favored : 82.00 % Rotamer: Outliers : 16.33 % Allowed : 24.00 % Favored : 59.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.24), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.088 0.012 PHEaA 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 323 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8393 (mp0) REVERT: A 6 LYS cc_start: 0.9083 (tttt) cc_final: 0.8713 (tttm) REVERT: A 7 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: K 104 GLU cc_start: 0.8638 (mp0) cc_final: 0.8311 (mp0) REVERT: K 107 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.8526 (m-80) REVERT: L 207 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: M 306 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8646 (tttt) REVERT: M 307 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.8086 (m-10) REVERT: B 4 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: T 306 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8739 (ttmt) REVERT: C 4 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: C 6 LYS cc_start: 0.8985 (tttt) cc_final: 0.8660 (tttm) REVERT: D 4 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7869 (tm-30) REVERT: m 304 GLU cc_start: 0.8660 (mp0) cc_final: 0.7943 (mp0) REVERT: n 404 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7932 (mt-10) REVERT: E 4 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8307 (mp0) REVERT: E 6 LYS cc_start: 0.9082 (tttt) cc_final: 0.8763 (tttp) REVERT: r 104 GLU cc_start: 0.8612 (mp0) cc_final: 0.8276 (mp0) REVERT: t 307 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.9208 (m-10) REVERT: u 404 GLU cc_start: 0.8655 (mm-30) cc_final: 0.7964 (mm-30) REVERT: u 406 LYS cc_start: 0.8975 (mptt) cc_final: 0.8593 (ttmt) REVERT: F 4 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: F 7 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8348 (m-10) REVERT: y 104 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7795 (tm-30) REVERT: y 107 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: z 207 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: 0 307 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: G 6 LYS cc_start: 0.9374 (tttt) cc_final: 0.8810 (tttm) REVERT: G 7 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: 6 207 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8069 (m-10) REVERT: 7 307 PHE cc_start: 0.9400 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: H 4 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7568 (tm-30) REVERT: H 6 LYS cc_start: 0.9352 (tttt) cc_final: 0.8942 (ttmt) REVERT: I 6 LYS cc_start: 0.9084 (tttt) cc_final: 0.8769 (tttm) REVERT: KA 204 GLU cc_start: 0.8567 (mp0) cc_final: 0.8364 (pm20) REVERT: LA 304 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8328 (pm20) REVERT: MA 404 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8246 (pm20) REVERT: QA 104 GLU cc_start: 0.8816 (pm20) cc_final: 0.8520 (pm20) REVERT: RA 204 GLU cc_start: 0.8881 (pm20) cc_final: 0.8563 (pm20) REVERT: SA 304 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: TA 404 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7563 (tm-30) REVERT: XA 55 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7766 (t80) REVERT: XA 56 LYS cc_start: 0.9161 (tmtt) cc_final: 0.8927 (tttm) REVERT: ZA 155 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7955 (t80) REVERT: ZA 156 LYS cc_start: 0.9391 (tmtt) cc_final: 0.9083 (tmtt) REVERT: aA 203 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.6837 (t80) REVERT: aA 204 GLU cc_start: 0.8391 (tp30) cc_final: 0.7898 (tm-30) REVERT: aA 206 LYS cc_start: 0.9162 (tttm) cc_final: 0.8903 (tttp) REVERT: bA 255 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7777 (t80) REVERT: bA 256 LYS cc_start: 0.9158 (tmtt) cc_final: 0.8934 (tmtt) REVERT: cA 302 LYS cc_start: 0.9123 (tmtt) cc_final: 0.8815 (tmtt) REVERT: cA 303 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.6315 (t80) REVERT: cA 304 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7876 (tm-30) REVERT: dA 355 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7628 (t80) REVERT: dA 356 LYS cc_start: 0.9015 (tmtt) cc_final: 0.8703 (tttm) REVERT: eA 406 LYS cc_start: 0.9382 (tttp) cc_final: 0.9154 (tttp) REVERT: fA 455 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7987 (t80) REVERT: fA 456 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9134 (tttm) REVERT: b 2 LYS cc_start: 0.9205 (ttmm) cc_final: 0.8983 (ttmm) REVERT: mA 55 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7261 (t80) REVERT: mA 56 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9148 (tttp) REVERT: oA 155 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7164 (t80) REVERT: oA 156 LYS cc_start: 0.9353 (tmtt) cc_final: 0.9058 (tttp) REVERT: pA 204 GLU cc_start: 0.8573 (tp30) cc_final: 0.8249 (tm-30) REVERT: qA 255 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.6844 (t80) REVERT: rA 302 LYS cc_start: 0.9142 (tmtt) cc_final: 0.8925 (tmtt) REVERT: rA 304 GLU cc_start: 0.8541 (tp30) cc_final: 0.8316 (tp30) REVERT: sA 355 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.6796 (t80) REVERT: tA 406 LYS cc_start: 0.9342 (tttp) cc_final: 0.8955 (tttp) REVERT: uA 455 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7200 (t80) REVERT: uA 456 LYS cc_start: 0.9405 (tmtt) cc_final: 0.9122 (tttp) REVERT: c 4 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8424 (tm-30) REVERT: 1A 56 LYS cc_start: 0.9322 (tmtt) cc_final: 0.9064 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: 3A 152 LYS cc_start: 0.9214 (tmtt) cc_final: 0.8919 (tmtt) REVERT: 3A 156 LYS cc_start: 0.9373 (tmtt) cc_final: 0.9061 (tmtt) REVERT: 4A 206 LYS cc_start: 0.9080 (tttm) cc_final: 0.8785 (tttm) REVERT: 5A 256 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8900 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9328 (tmtt) cc_final: 0.8668 (tmtt) REVERT: GB 56 LYS cc_start: 0.9338 (tmtt) cc_final: 0.8996 (tmtt) REVERT: HB 105 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8515 (t80) REVERT: IB 156 LYS cc_start: 0.9364 (tmtt) cc_final: 0.9161 (tmtt) REVERT: LB 302 LYS cc_start: 0.9190 (tmtt) cc_final: 0.8806 (ttmm) REVERT: OB 456 LYS cc_start: 0.9381 (tmtt) cc_final: 0.9179 (tmtt) REVERT: e 4 GLU cc_start: 0.8677 (tp30) cc_final: 0.8269 (tm-30) REVERT: VB 55 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7711 (t80) REVERT: XB 157 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7713 (t80) REVERT: YB 204 GLU cc_start: 0.8596 (tp30) cc_final: 0.8240 (tm-30) REVERT: aB 302 LYS cc_start: 0.9172 (tmtt) cc_final: 0.8678 (tmtt) REVERT: cB 402 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8754 (ttmm) outliers start: 98 outliers final: 40 residues processed: 351 average time/residue: 0.3729 time to fit residues: 155.5520 Evaluate side-chains 388 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 312 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain F residue 4 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain 7 residue 307 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain SA residue 304 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 405 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.178 8700 Z= 2.760 Angle : 2.723 17.081 11300 Z= 1.307 Chirality : 0.136 0.333 800 Planarity : 0.011 0.040 1500 Dihedral : 26.861 87.799 1021 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 120.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.00 % Favored : 77.00 % Rotamer: Outliers : 18.83 % Allowed : 29.17 % Favored : 52.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.13 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.093 0.011 PHEaA 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 316 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: A 6 LYS cc_start: 0.9092 (tttt) cc_final: 0.8734 (tttm) REVERT: A 7 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: K 104 GLU cc_start: 0.8633 (mp0) cc_final: 0.8432 (mp0) REVERT: K 107 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: L 207 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: M 306 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8727 (ttpt) REVERT: M 307 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8131 (m-10) REVERT: B 4 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: C 4 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8556 (mp0) REVERT: C 6 LYS cc_start: 0.9093 (tttt) cc_final: 0.8727 (tttm) REVERT: k 104 GLU cc_start: 0.8860 (mp0) cc_final: 0.8634 (mp0) REVERT: E 4 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: E 6 LYS cc_start: 0.9040 (tttt) cc_final: 0.8763 (tttp) REVERT: r 104 GLU cc_start: 0.8652 (mp0) cc_final: 0.8370 (mp0) REVERT: t 307 PHE cc_start: 0.9472 (OUTLIER) cc_final: 0.9241 (m-10) REVERT: u 404 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7817 (mm-30) REVERT: u 406 LYS cc_start: 0.9013 (mptt) cc_final: 0.8559 (ttmt) REVERT: F 7 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8286 (m-10) REVERT: y 107 PHE cc_start: 0.9350 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: z 206 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8861 (ttpt) REVERT: z 207 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8213 (m-10) REVERT: 0 307 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8628 (m-80) REVERT: 1 404 GLU cc_start: 0.8893 (mp0) cc_final: 0.8618 (mp0) REVERT: G 6 LYS cc_start: 0.9433 (tttt) cc_final: 0.8873 (tttm) REVERT: G 7 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.7873 (m-10) REVERT: 6 206 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8761 (ttpt) REVERT: 6 207 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: H 4 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7716 (tm-30) REVERT: H 6 LYS cc_start: 0.9309 (tttt) cc_final: 0.8869 (ttmt) REVERT: I 4 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8431 (mp0) REVERT: I 6 LYS cc_start: 0.9041 (tttt) cc_final: 0.8740 (tttm) REVERT: KA 204 GLU cc_start: 0.8694 (mp0) cc_final: 0.8408 (pm20) REVERT: LA 304 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8358 (pm20) REVERT: MA 404 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8339 (pm20) REVERT: J 4 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7694 (tm-30) REVERT: QA 104 GLU cc_start: 0.8796 (pm20) cc_final: 0.8348 (pm20) REVERT: RA 204 GLU cc_start: 0.8940 (pm20) cc_final: 0.8602 (pm20) REVERT: SA 304 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: TA 404 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7798 (tm-30) REVERT: a 4 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8041 (tp30) REVERT: XA 55 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7886 (t80) REVERT: XA 56 LYS cc_start: 0.9215 (tmtt) cc_final: 0.8905 (tttp) REVERT: YA 104 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8145 (tp30) REVERT: ZA 155 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7943 (t80) REVERT: ZA 156 LYS cc_start: 0.9411 (tmtt) cc_final: 0.9175 (tttm) REVERT: aA 204 GLU cc_start: 0.8218 (tp30) cc_final: 0.8018 (tm-30) REVERT: aA 206 LYS cc_start: 0.9132 (tttm) cc_final: 0.8384 (tttp) REVERT: bA 255 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7767 (t80) REVERT: bA 256 LYS cc_start: 0.9211 (tmtt) cc_final: 0.8876 (tmtt) REVERT: cA 303 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.6686 (t80) REVERT: cA 304 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: dA 355 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7672 (t80) REVERT: dA 356 LYS cc_start: 0.9171 (tmtt) cc_final: 0.8816 (tttp) REVERT: eA 403 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.7364 (t80) REVERT: eA 406 LYS cc_start: 0.9393 (tttp) cc_final: 0.9184 (tttp) REVERT: fA 455 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8064 (t80) REVERT: fA 456 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9043 (tttp) REVERT: mA 55 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7261 (t80) REVERT: mA 56 LYS cc_start: 0.9393 (tmtt) cc_final: 0.9137 (tttp) REVERT: oA 156 LYS cc_start: 0.9326 (tmtt) cc_final: 0.9106 (tttp) REVERT: qA 252 LYS cc_start: 0.8971 (tmtt) cc_final: 0.8758 (tmtt) REVERT: rA 304 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8174 (tp30) REVERT: rA 305 PHE cc_start: 0.8952 (t80) cc_final: 0.8634 (t80) REVERT: sA 352 LYS cc_start: 0.9013 (tmtt) cc_final: 0.8806 (tmtt) REVERT: sA 355 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.6882 (t80) REVERT: sA 356 LYS cc_start: 0.9074 (tmtt) cc_final: 0.8774 (tttm) REVERT: uA 455 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.6868 (t80) REVERT: uA 456 LYS cc_start: 0.9384 (tmtt) cc_final: 0.9066 (tttp) REVERT: c 4 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: 1A 56 LYS cc_start: 0.9384 (tmtt) cc_final: 0.9050 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8464 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9334 (tmtt) cc_final: 0.8961 (tmtt) REVERT: 4A 206 LYS cc_start: 0.9132 (tttm) cc_final: 0.8875 (tttm) REVERT: 7A 356 LYS cc_start: 0.9351 (tmtt) cc_final: 0.8801 (tmtt) REVERT: GB 56 LYS cc_start: 0.9330 (tmtt) cc_final: 0.9098 (tmtt) REVERT: HB 105 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8312 (t80) REVERT: IB 156 LYS cc_start: 0.9306 (tmtt) cc_final: 0.9066 (tmtt) REVERT: JB 204 GLU cc_start: 0.8660 (tp30) cc_final: 0.8191 (pm20) REVERT: KB 256 LYS cc_start: 0.9092 (tmtt) cc_final: 0.8736 (tmtt) REVERT: LB 302 LYS cc_start: 0.9191 (tmtt) cc_final: 0.8815 (ttmm) REVERT: LB 305 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8305 (t80) REVERT: VB 55 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7726 (t80) REVERT: XB 155 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7754 (t80) REVERT: XB 157 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7488 (t80) REVERT: YB 204 GLU cc_start: 0.8565 (tp30) cc_final: 0.8114 (tm-30) REVERT: aB 302 LYS cc_start: 0.9171 (tmtt) cc_final: 0.8532 (ttmm) REVERT: aB 305 PHE cc_start: 0.8909 (t80) cc_final: 0.8652 (t80) REVERT: bB 352 LYS cc_start: 0.9013 (tmtt) cc_final: 0.8509 (pptt) REVERT: cB 402 LYS cc_start: 0.9148 (tmtt) cc_final: 0.8741 (ttmm) outliers start: 113 outliers final: 57 residues processed: 344 average time/residue: 0.3921 time to fit residues: 160.6001 Evaluate side-chains 412 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 314 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain t residue 307 PHE Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain I residue 4 GLU Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain SA residue 304 GLU Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 303 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 4 GLU Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain IB residue 155 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain LB residue 305 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain OB residue 455 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.6448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.158 8700 Z= 2.767 Angle : 2.721 18.342 11300 Z= 1.304 Chirality : 0.137 0.334 800 Planarity : 0.011 0.039 1500 Dihedral : 26.672 89.878 1021 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 118.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.75 % Favored : 76.25 % Rotamer: Outliers : 19.67 % Allowed : 31.50 % Favored : 48.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.090 0.011 PHEaA 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 321 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: A 6 LYS cc_start: 0.9086 (tttt) cc_final: 0.8658 (tttm) REVERT: A 7 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.8144 (m-10) REVERT: K 104 GLU cc_start: 0.8643 (mp0) cc_final: 0.8406 (mp0) REVERT: K 107 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: L 207 PHE cc_start: 0.9371 (OUTLIER) cc_final: 0.8894 (m-80) REVERT: M 306 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8630 (tttt) REVERT: M 307 PHE cc_start: 0.9425 (OUTLIER) cc_final: 0.8100 (m-10) REVERT: B 4 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: C 4 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8537 (mp0) REVERT: C 6 LYS cc_start: 0.9131 (tttt) cc_final: 0.8900 (ttmt) REVERT: Y 106 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8850 (ttmt) REVERT: k 104 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: m 304 GLU cc_start: 0.8626 (mp0) cc_final: 0.8403 (mp0) REVERT: E 4 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: E 6 LYS cc_start: 0.9045 (tttt) cc_final: 0.8769 (tttp) REVERT: r 104 GLU cc_start: 0.8653 (mp0) cc_final: 0.8358 (mp0) REVERT: u 404 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8135 (mm-30) REVERT: u 406 LYS cc_start: 0.8997 (mptt) cc_final: 0.8554 (ttmt) REVERT: F 7 PHE cc_start: 0.9399 (OUTLIER) cc_final: 0.8303 (m-10) REVERT: y 104 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7809 (tm-30) REVERT: y 107 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: z 206 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8866 (ttpt) REVERT: z 207 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: 0 307 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.8599 (m-80) REVERT: G 7 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: 6 206 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8794 (ttpt) REVERT: 6 207 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8086 (m-10) REVERT: H 4 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: H 6 LYS cc_start: 0.9312 (tttt) cc_final: 0.8880 (ttmt) REVERT: I 6 LYS cc_start: 0.9042 (tttt) cc_final: 0.8756 (tttm) REVERT: JA 104 GLU cc_start: 0.4459 (OUTLIER) cc_final: 0.3628 (pm20) REVERT: KA 204 GLU cc_start: 0.8636 (mp0) cc_final: 0.8415 (pm20) REVERT: LA 304 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8349 (pm20) REVERT: J 4 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: RA 204 GLU cc_start: 0.8952 (pm20) cc_final: 0.8565 (pm20) REVERT: TA 404 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7871 (tm-30) REVERT: a 3 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.7610 (t80) REVERT: a 4 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8026 (tp30) REVERT: XA 52 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8873 (tmtt) REVERT: XA 55 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7892 (t80) REVERT: XA 56 LYS cc_start: 0.9250 (tmtt) cc_final: 0.8923 (tttp) REVERT: YA 104 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8270 (tp30) REVERT: ZA 152 LYS cc_start: 0.9085 (tmtt) cc_final: 0.8845 (tmtt) REVERT: ZA 155 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7987 (t80) REVERT: ZA 156 LYS cc_start: 0.9400 (tmtt) cc_final: 0.9154 (tttm) REVERT: aA 203 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8278 (t80) REVERT: aA 206 LYS cc_start: 0.9141 (tttm) cc_final: 0.8508 (tttp) REVERT: bA 255 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7836 (t80) REVERT: cA 302 LYS cc_start: 0.9226 (tmtt) cc_final: 0.9002 (tmtt) REVERT: cA 303 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.6948 (t80) REVERT: cA 304 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: dA 355 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7680 (t80) REVERT: eA 403 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.7203 (t80) REVERT: eA 406 LYS cc_start: 0.9397 (tttp) cc_final: 0.9189 (tttp) REVERT: fA 455 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.8089 (t80) REVERT: fA 456 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9095 (tttp) REVERT: mA 55 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.6996 (t80) REVERT: mA 56 LYS cc_start: 0.9356 (tmtt) cc_final: 0.9102 (tttp) REVERT: oA 156 LYS cc_start: 0.9330 (tmtt) cc_final: 0.9074 (tttp) REVERT: qA 252 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8864 (tmtt) REVERT: qA 256 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8877 (tmtt) REVERT: rA 304 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8156 (tm-30) REVERT: rA 305 PHE cc_start: 0.8948 (t80) cc_final: 0.8525 (t80) REVERT: sA 355 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.6948 (t80) REVERT: sA 356 LYS cc_start: 0.9038 (tmtt) cc_final: 0.8751 (tttm) REVERT: uA 455 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.6875 (t80) REVERT: uA 456 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9071 (tttp) REVERT: 1A 56 LYS cc_start: 0.9351 (tmtt) cc_final: 0.9012 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: 4A 205 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8137 (t80) REVERT: 4A 206 LYS cc_start: 0.9161 (tttm) cc_final: 0.8742 (tttm) REVERT: 5A 256 LYS cc_start: 0.9146 (tmtt) cc_final: 0.8734 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9070 (tttm) REVERT: GB 56 LYS cc_start: 0.9353 (tmtt) cc_final: 0.9075 (tmtt) REVERT: HB 105 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8342 (t80) REVERT: IB 156 LYS cc_start: 0.9280 (tmtt) cc_final: 0.9072 (tmtt) REVERT: LB 302 LYS cc_start: 0.9200 (tmtt) cc_final: 0.8854 (ttmm) REVERT: VB 55 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7676 (t80) REVERT: XB 152 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8512 (pptt) REVERT: XB 155 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7774 (t80) REVERT: XB 157 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7511 (t80) REVERT: YB 204 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8208 (tp30) REVERT: YB 205 PHE cc_start: 0.8965 (t80) cc_final: 0.8480 (t80) REVERT: ZB 252 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8393 (pptt) REVERT: ZB 256 LYS cc_start: 0.9308 (tmtt) cc_final: 0.9086 (tttp) REVERT: aB 305 PHE cc_start: 0.8946 (t80) cc_final: 0.8740 (t80) REVERT: bB 352 LYS cc_start: 0.9101 (tmtt) cc_final: 0.8484 (pptt) REVERT: cB 402 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8748 (ttmm) REVERT: dB 452 LYS cc_start: 0.9073 (tmtt) cc_final: 0.8408 (pptt) outliers start: 118 outliers final: 56 residues processed: 351 average time/residue: 0.3712 time to fit residues: 155.0157 Evaluate side-chains 423 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 321 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain J residue 6 LYS Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain OB residue 455 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.169 8700 Z= 2.765 Angle : 2.716 19.367 11300 Z= 1.303 Chirality : 0.137 0.340 800 Planarity : 0.011 0.040 1500 Dihedral : 26.506 89.816 1021 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 117.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.25 % Favored : 75.75 % Rotamer: Outliers : 20.33 % Allowed : 30.50 % Favored : 49.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.089 0.011 PHE c 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 321 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: A 6 LYS cc_start: 0.9087 (tttt) cc_final: 0.8744 (tttm) REVERT: A 7 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: K 104 GLU cc_start: 0.8647 (mp0) cc_final: 0.8392 (mp0) REVERT: K 107 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: L 207 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.9021 (m-80) REVERT: M 304 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: M 306 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8651 (tttt) REVERT: M 307 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: B 4 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: U 404 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: C 4 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: C 6 LYS cc_start: 0.9152 (tttt) cc_final: 0.8918 (ttmt) REVERT: Y 106 LYS cc_start: 0.9122 (mtpt) cc_final: 0.8856 (ttmt) REVERT: D 4 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7936 (tm-30) REVERT: k 104 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: E 4 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: E 6 LYS cc_start: 0.9039 (tttt) cc_final: 0.8756 (tttp) REVERT: r 104 GLU cc_start: 0.8687 (mp0) cc_final: 0.8403 (mp0) REVERT: u 404 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8031 (mm-30) REVERT: u 406 LYS cc_start: 0.8941 (mptt) cc_final: 0.8440 (ttmt) REVERT: F 7 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.8234 (m-10) REVERT: y 107 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8424 (m-80) REVERT: z 206 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8864 (ttpt) REVERT: z 207 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8201 (m-10) REVERT: 0 307 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: G 6 LYS cc_start: 0.9399 (tttt) cc_final: 0.8833 (tttm) REVERT: G 7 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.7818 (m-10) REVERT: 6 206 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8803 (ttpt) REVERT: 6 207 PHE cc_start: 0.9243 (OUTLIER) cc_final: 0.8083 (m-10) REVERT: H 4 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: H 6 LYS cc_start: 0.9311 (tttt) cc_final: 0.8989 (ttmt) REVERT: JA 104 GLU cc_start: 0.4475 (OUTLIER) cc_final: 0.3775 (pm20) REVERT: LA 304 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8384 (pm20) REVERT: J 4 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: RA 204 GLU cc_start: 0.8955 (pm20) cc_final: 0.8537 (pm20) REVERT: SA 304 GLU cc_start: 0.8927 (pm20) cc_final: 0.8716 (pm20) REVERT: TA 404 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7931 (tm-30) REVERT: a 3 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.7599 (t80) REVERT: a 4 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: XA 52 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8800 (tmtt) REVERT: XA 55 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7835 (t80) REVERT: XA 56 LYS cc_start: 0.9248 (tmtt) cc_final: 0.8926 (tttp) REVERT: YA 103 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8149 (t80) REVERT: YA 104 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8120 (tp30) REVERT: ZA 155 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.8021 (t80) REVERT: ZA 156 LYS cc_start: 0.9403 (tmtt) cc_final: 0.9158 (tttm) REVERT: aA 203 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8305 (t80) REVERT: cA 303 PHE cc_start: 0.8923 (OUTLIER) cc_final: 0.7083 (t80) REVERT: cA 304 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: dA 355 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7664 (t80) REVERT: eA 403 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8444 (t80) REVERT: eA 404 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7825 (tm-30) REVERT: eA 406 LYS cc_start: 0.9408 (tttp) cc_final: 0.9181 (tttp) REVERT: fA 455 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8027 (t80) REVERT: fA 456 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.9081 (tttp) REVERT: mA 55 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.6972 (t80) REVERT: mA 56 LYS cc_start: 0.9346 (tmtt) cc_final: 0.9076 (tttp) REVERT: oA 152 LYS cc_start: 0.8968 (tmtt) cc_final: 0.8690 (tmtt) REVERT: oA 156 LYS cc_start: 0.9335 (tmtt) cc_final: 0.9083 (tttp) REVERT: rA 304 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8133 (tm-30) REVERT: rA 305 PHE cc_start: 0.8938 (t80) cc_final: 0.8515 (t80) REVERT: sA 355 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.6979 (t80) REVERT: sA 356 LYS cc_start: 0.9019 (tmtt) cc_final: 0.8732 (tttm) REVERT: uA 456 LYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9133 (tttp) REVERT: 1A 56 LYS cc_start: 0.9367 (tmtt) cc_final: 0.8988 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9362 (tmtt) cc_final: 0.9049 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.8192 (t80) REVERT: 4A 206 LYS cc_start: 0.9186 (tttm) cc_final: 0.8738 (tttm) REVERT: 5A 256 LYS cc_start: 0.9192 (tmtt) cc_final: 0.8895 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9041 (tttm) REVERT: d 5 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8433 (t80) REVERT: HB 105 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8288 (t80) REVERT: IB 156 LYS cc_start: 0.9307 (tmtt) cc_final: 0.9093 (tmtt) REVERT: JB 204 GLU cc_start: 0.8765 (tp30) cc_final: 0.8142 (pm20) REVERT: KB 256 LYS cc_start: 0.9111 (tmtt) cc_final: 0.8771 (tmtt) REVERT: LB 302 LYS cc_start: 0.9231 (tmtt) cc_final: 0.8903 (ttmm) REVERT: LB 306 LYS cc_start: 0.9384 (tttm) cc_final: 0.9165 (tttm) REVERT: VB 52 LYS cc_start: 0.9045 (tmtt) cc_final: 0.8466 (pptt) REVERT: XB 152 LYS cc_start: 0.9024 (tmtt) cc_final: 0.8525 (pptt) REVERT: XB 157 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.7687 (t80) REVERT: YB 204 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8187 (tp30) REVERT: YB 205 PHE cc_start: 0.8964 (t80) cc_final: 0.8484 (t80) REVERT: ZB 252 LYS cc_start: 0.9072 (tmtt) cc_final: 0.8283 (pptt) REVERT: aB 305 PHE cc_start: 0.9001 (t80) cc_final: 0.8791 (t80) REVERT: bB 352 LYS cc_start: 0.9116 (tmtt) cc_final: 0.8475 (pptt) REVERT: cB 402 LYS cc_start: 0.9164 (tmtt) cc_final: 0.8716 (ttmm) REVERT: dB 452 LYS cc_start: 0.9111 (tmtt) cc_final: 0.8438 (pptt) outliers start: 122 outliers final: 67 residues processed: 354 average time/residue: 0.3657 time to fit residues: 154.7189 Evaluate side-chains 432 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 319 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain U residue 404 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain OB residue 455 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 303 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.170 8700 Z= 2.763 Angle : 2.721 20.162 11300 Z= 1.306 Chirality : 0.138 0.345 800 Planarity : 0.011 0.040 1500 Dihedral : 26.356 89.855 1021 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 117.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.75 % Favored : 75.25 % Rotamer: Outliers : 21.67 % Allowed : 30.50 % Favored : 47.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.32), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.092 0.011 PHEaA 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 320 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: A 6 LYS cc_start: 0.9074 (tttt) cc_final: 0.8726 (tttm) REVERT: A 7 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8358 (m-80) REVERT: K 104 GLU cc_start: 0.8650 (mp0) cc_final: 0.8381 (mp0) REVERT: K 107 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: L 207 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.9007 (m-80) REVERT: M 304 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: M 306 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8667 (tttt) REVERT: M 307 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.7996 (m-10) REVERT: B 4 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: U 404 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: C 4 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: C 6 LYS cc_start: 0.9171 (tttt) cc_final: 0.8788 (tttm) REVERT: Y 106 LYS cc_start: 0.9161 (mtpt) cc_final: 0.8880 (ttmt) REVERT: D 4 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: k 104 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: E 4 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: E 6 LYS cc_start: 0.9020 (tttt) cc_final: 0.8738 (tttp) REVERT: r 104 GLU cc_start: 0.8679 (mp0) cc_final: 0.8395 (mp0) REVERT: u 404 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: u 406 LYS cc_start: 0.8932 (mptt) cc_final: 0.8488 (ttmt) REVERT: F 7 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.8222 (m-10) REVERT: y 104 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: y 107 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8427 (m-80) REVERT: z 206 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8861 (ttpt) REVERT: z 207 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8199 (m-10) REVERT: 0 307 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: G 6 LYS cc_start: 0.9405 (tttt) cc_final: 0.8835 (tttm) REVERT: G 7 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.7793 (m-10) REVERT: 6 206 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8834 (ttpt) REVERT: 6 207 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8096 (m-10) REVERT: H 4 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: H 6 LYS cc_start: 0.9298 (tttt) cc_final: 0.8860 (ttmt) REVERT: JA 104 GLU cc_start: 0.4520 (OUTLIER) cc_final: 0.3860 (pm20) REVERT: LA 304 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8429 (pm20) REVERT: J 4 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: QA 104 GLU cc_start: 0.8881 (pm20) cc_final: 0.7495 (mm-30) REVERT: RA 204 GLU cc_start: 0.8960 (pm20) cc_final: 0.8522 (pm20) REVERT: SA 304 GLU cc_start: 0.8911 (pm20) cc_final: 0.8654 (pm20) REVERT: TA 404 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7960 (tm-30) REVERT: a 3 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.7589 (t80) REVERT: a 4 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: XA 52 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8758 (tmtt) REVERT: XA 55 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7869 (t80) REVERT: XA 56 LYS cc_start: 0.9264 (tmtt) cc_final: 0.8946 (tttp) REVERT: YA 103 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8141 (t80) REVERT: YA 104 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8039 (tp30) REVERT: ZA 155 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.7982 (t80) REVERT: ZA 156 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.9111 (tttm) REVERT: aA 203 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8245 (t80) REVERT: bA 255 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7725 (t80) REVERT: cA 304 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8215 (tm-30) REVERT: dA 355 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7665 (t80) REVERT: eA 403 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8427 (t80) REVERT: eA 404 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7830 (tm-30) REVERT: eA 406 LYS cc_start: 0.9395 (tttp) cc_final: 0.9186 (tttp) REVERT: fA 455 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8104 (t80) REVERT: fA 456 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9101 (tttm) REVERT: mA 55 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.6976 (t80) REVERT: mA 56 LYS cc_start: 0.9338 (tmtt) cc_final: 0.9066 (tttp) REVERT: oA 152 LYS cc_start: 0.8979 (tmtt) cc_final: 0.8744 (tmtt) REVERT: oA 156 LYS cc_start: 0.9338 (tmtt) cc_final: 0.9074 (tttp) REVERT: qA 256 LYS cc_start: 0.9195 (tmtt) cc_final: 0.8957 (tttm) REVERT: rA 304 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: rA 305 PHE cc_start: 0.8941 (t80) cc_final: 0.8578 (t80) REVERT: sA 355 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7134 (t80) REVERT: sA 356 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8683 (tttm) REVERT: uA 456 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9109 (tttp) REVERT: 1A 56 LYS cc_start: 0.9367 (tmtt) cc_final: 0.9022 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8462 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9350 (tmtt) cc_final: 0.8971 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8141 (t80) REVERT: 4A 206 LYS cc_start: 0.9185 (tttm) cc_final: 0.8822 (tttm) REVERT: 5A 256 LYS cc_start: 0.9205 (tmtt) cc_final: 0.8876 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.9032 (tttm) REVERT: d 5 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8391 (t80) REVERT: HB 105 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8290 (t80) REVERT: IB 156 LYS cc_start: 0.9274 (tmtt) cc_final: 0.9044 (tmtt) REVERT: JB 205 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8420 (t80) REVERT: JB 206 LYS cc_start: 0.9442 (tttm) cc_final: 0.9083 (tttm) REVERT: KB 256 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8792 (tmtt) REVERT: LB 302 LYS cc_start: 0.9232 (tmtt) cc_final: 0.8903 (ttmm) REVERT: LB 306 LYS cc_start: 0.9382 (tttm) cc_final: 0.9158 (tttm) REVERT: MB 356 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8832 (tmtt) REVERT: VB 52 LYS cc_start: 0.9066 (tmtt) cc_final: 0.8426 (pptt) REVERT: XB 152 LYS cc_start: 0.9019 (tmtt) cc_final: 0.8516 (pptt) REVERT: XB 157 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7678 (t80) REVERT: YB 204 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8268 (mt-10) REVERT: YB 205 PHE cc_start: 0.8981 (t80) cc_final: 0.8599 (t80) REVERT: ZB 252 LYS cc_start: 0.9115 (tmtt) cc_final: 0.8481 (pptt) REVERT: aB 304 GLU cc_start: 0.8803 (tp30) cc_final: 0.8119 (tm-30) REVERT: aB 305 PHE cc_start: 0.9012 (t80) cc_final: 0.8618 (t80) REVERT: bB 352 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8511 (pptt) REVERT: dB 452 LYS cc_start: 0.9133 (tmtt) cc_final: 0.8445 (pptt) outliers start: 130 outliers final: 66 residues processed: 354 average time/residue: 0.3631 time to fit residues: 153.2353 Evaluate side-chains 437 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 319 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain U residue 404 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain sA residue 356 LYS Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 1A residue 55 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain GB residue 55 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.6736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.163 8700 Z= 2.763 Angle : 2.722 20.348 11300 Z= 1.307 Chirality : 0.138 0.345 800 Planarity : 0.011 0.042 1500 Dihedral : 26.287 89.994 1021 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 116.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.75 % Favored : 75.25 % Rotamer: Outliers : 22.00 % Allowed : 31.17 % Favored : 46.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.096 0.011 PHEaA 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 320 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8425 (mp0) REVERT: A 6 LYS cc_start: 0.9074 (tttt) cc_final: 0.8724 (tttm) REVERT: A 7 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: K 104 GLU cc_start: 0.8651 (mp0) cc_final: 0.8378 (mp0) REVERT: K 107 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: L 207 PHE cc_start: 0.9394 (OUTLIER) cc_final: 0.8938 (m-80) REVERT: M 304 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: M 306 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8693 (tttt) REVERT: M 307 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.7995 (m-10) REVERT: B 4 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: U 404 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: C 4 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: C 6 LYS cc_start: 0.9174 (tttt) cc_final: 0.8795 (tttp) REVERT: Y 106 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8886 (ttmt) REVERT: D 4 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: k 104 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: E 4 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: E 6 LYS cc_start: 0.9011 (tttt) cc_final: 0.8732 (tttp) REVERT: r 104 GLU cc_start: 0.8682 (mp0) cc_final: 0.8400 (mp0) REVERT: u 404 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: u 406 LYS cc_start: 0.8932 (mptt) cc_final: 0.8486 (ttmt) REVERT: F 7 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.8295 (m-10) REVERT: y 104 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: y 107 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8418 (m-80) REVERT: z 206 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8868 (ttpt) REVERT: z 207 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8191 (m-10) REVERT: 0 307 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.8597 (m-80) REVERT: G 6 LYS cc_start: 0.9401 (tttt) cc_final: 0.8832 (tttm) REVERT: G 7 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: 6 206 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8832 (ttpt) REVERT: 6 207 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8090 (m-10) REVERT: H 4 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7787 (tm-30) REVERT: H 6 LYS cc_start: 0.9294 (tttt) cc_final: 0.8858 (ttmt) REVERT: EA 302 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8730 (ttmm) REVERT: JA 104 GLU cc_start: 0.4483 (OUTLIER) cc_final: 0.3776 (pm20) REVERT: LA 304 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8329 (pm20) REVERT: J 4 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: QA 104 GLU cc_start: 0.8862 (pm20) cc_final: 0.7496 (mm-30) REVERT: RA 204 GLU cc_start: 0.8966 (pm20) cc_final: 0.8528 (pm20) REVERT: SA 304 GLU cc_start: 0.8905 (pm20) cc_final: 0.8553 (pm20) REVERT: TA 404 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7952 (tm-30) REVERT: a 3 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.7528 (t80) REVERT: a 4 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: XA 52 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8753 (tmtt) REVERT: XA 55 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7853 (t80) REVERT: XA 56 LYS cc_start: 0.9254 (tmtt) cc_final: 0.8928 (tttp) REVERT: YA 103 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8137 (t80) REVERT: YA 104 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8043 (tp30) REVERT: ZA 155 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8116 (t80) REVERT: ZA 156 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9125 (tttp) REVERT: aA 203 PHE cc_start: 0.8887 (OUTLIER) cc_final: 0.8232 (t80) REVERT: bA 255 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7893 (t80) REVERT: cA 303 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.7148 (t80) REVERT: cA 304 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: dA 355 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7695 (t80) REVERT: eA 403 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8515 (t80) REVERT: eA 404 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8029 (tm-30) REVERT: eA 406 LYS cc_start: 0.9383 (tttp) cc_final: 0.9180 (tttp) REVERT: fA 455 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8097 (t80) REVERT: fA 456 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9104 (tttm) REVERT: mA 55 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.6983 (t80) REVERT: mA 56 LYS cc_start: 0.9317 (tmtt) cc_final: 0.9002 (tttp) REVERT: oA 152 LYS cc_start: 0.8989 (tmtt) cc_final: 0.8776 (tmtt) REVERT: oA 156 LYS cc_start: 0.9342 (tmtt) cc_final: 0.9072 (tttp) REVERT: rA 304 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: rA 305 PHE cc_start: 0.8943 (t80) cc_final: 0.8575 (t80) REVERT: sA 355 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7095 (t80) REVERT: sA 356 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8752 (tttm) REVERT: uA 456 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9108 (tttp) REVERT: 1A 56 LYS cc_start: 0.9394 (tmtt) cc_final: 0.9056 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8502 (tm-30) REVERT: 3A 156 LYS cc_start: 0.9346 (tmtt) cc_final: 0.8919 (tmtt) REVERT: 4A 205 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8158 (t80) REVERT: 4A 206 LYS cc_start: 0.9187 (tttm) cc_final: 0.8747 (tttm) REVERT: 5A 256 LYS cc_start: 0.9215 (tmtt) cc_final: 0.8871 (tmtt) REVERT: 6A 302 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8862 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9018 (tttm) REVERT: d 5 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8439 (t80) REVERT: HB 105 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8351 (t80) REVERT: IB 156 LYS cc_start: 0.9271 (tmtt) cc_final: 0.9024 (tmtt) REVERT: JB 205 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8045 (t80) REVERT: JB 206 LYS cc_start: 0.9472 (tttm) cc_final: 0.9120 (tttm) REVERT: KB 256 LYS cc_start: 0.9136 (tmtt) cc_final: 0.8805 (tmtt) REVERT: LB 302 LYS cc_start: 0.9231 (tmtt) cc_final: 0.8901 (ttmm) REVERT: LB 306 LYS cc_start: 0.9379 (tttm) cc_final: 0.9135 (tttm) REVERT: VB 52 LYS cc_start: 0.9029 (tmtt) cc_final: 0.8437 (pptt) REVERT: XB 152 LYS cc_start: 0.9061 (tmtt) cc_final: 0.8524 (pptt) REVERT: XB 157 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7647 (t80) REVERT: YB 204 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: YB 205 PHE cc_start: 0.8982 (t80) cc_final: 0.8614 (t80) REVERT: ZB 252 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8477 (pptt) REVERT: aB 305 PHE cc_start: 0.9018 (t80) cc_final: 0.8731 (t80) REVERT: bB 352 LYS cc_start: 0.9099 (tmtt) cc_final: 0.8414 (pptt) REVERT: dB 452 LYS cc_start: 0.9100 (tmtt) cc_final: 0.8437 (pptt) outliers start: 132 outliers final: 67 residues processed: 355 average time/residue: 0.3593 time to fit residues: 152.3118 Evaluate side-chains 442 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 320 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain U residue 404 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain D residue 4 GLU Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 302 LYS Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain sA residue 356 LYS Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 302 LYS Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.6787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.154 8700 Z= 2.767 Angle : 2.724 20.332 11300 Z= 1.309 Chirality : 0.138 0.354 800 Planarity : 0.011 0.041 1500 Dihedral : 26.235 89.812 1021 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 117.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 22.00 % Allowed : 31.00 % Favored : 47.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.096 0.011 PHEaA 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 322 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8423 (mp0) REVERT: A 6 LYS cc_start: 0.9077 (tttt) cc_final: 0.8724 (tttm) REVERT: A 7 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: K 104 GLU cc_start: 0.8647 (mp0) cc_final: 0.8364 (mp0) REVERT: K 107 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8474 (m-80) REVERT: L 207 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8893 (m-80) REVERT: M 304 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: M 306 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8691 (tttt) REVERT: M 307 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.7999 (m-10) REVERT: B 4 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: U 404 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7862 (mm-30) REVERT: C 4 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8568 (mp0) REVERT: C 6 LYS cc_start: 0.9178 (tttt) cc_final: 0.8817 (tttm) REVERT: Y 106 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8884 (ttmt) REVERT: k 104 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: m 304 GLU cc_start: 0.8620 (mp0) cc_final: 0.8419 (mp0) REVERT: E 4 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: E 6 LYS cc_start: 0.8996 (tttt) cc_final: 0.8715 (tttp) REVERT: r 104 GLU cc_start: 0.8689 (mp0) cc_final: 0.8404 (mp0) REVERT: u 404 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: u 406 LYS cc_start: 0.8979 (mptt) cc_final: 0.8542 (ttmt) REVERT: F 7 PHE cc_start: 0.9437 (OUTLIER) cc_final: 0.8274 (m-10) REVERT: y 104 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: y 107 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: z 206 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8867 (ttpt) REVERT: z 207 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8184 (m-10) REVERT: 0 307 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8593 (m-80) REVERT: G 6 LYS cc_start: 0.9391 (tttt) cc_final: 0.8855 (tttm) REVERT: G 7 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.7874 (m-10) REVERT: 6 206 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8839 (ttpt) REVERT: 6 207 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8089 (m-10) REVERT: H 4 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: H 6 LYS cc_start: 0.9297 (tttt) cc_final: 0.8863 (ttmt) REVERT: JA 104 GLU cc_start: 0.4491 (OUTLIER) cc_final: 0.3831 (pm20) REVERT: LA 304 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8308 (pm20) REVERT: J 4 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7841 (tm-30) REVERT: QA 104 GLU cc_start: 0.8869 (pm20) cc_final: 0.7495 (mm-30) REVERT: RA 204 GLU cc_start: 0.8970 (pm20) cc_final: 0.8521 (pm20) REVERT: SA 304 GLU cc_start: 0.8903 (pm20) cc_final: 0.8604 (pm20) REVERT: TA 404 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7953 (tm-30) REVERT: a 3 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8474 (t80) REVERT: a 4 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8059 (tp30) REVERT: XA 52 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8751 (tmtt) REVERT: XA 55 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7871 (t80) REVERT: XA 56 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8932 (tttp) REVERT: YA 103 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8138 (t80) REVERT: YA 104 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8035 (tp30) REVERT: ZA 155 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8048 (t80) REVERT: ZA 156 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9136 (tttp) REVERT: aA 203 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8353 (t80) REVERT: bA 255 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7897 (t80) REVERT: cA 303 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.7422 (t80) REVERT: cA 304 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8066 (tp30) REVERT: dA 355 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7712 (t80) REVERT: eA 403 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8513 (t80) REVERT: eA 404 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8036 (tm-30) REVERT: fA 455 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8132 (t80) REVERT: fA 456 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.9112 (tttm) REVERT: mA 56 LYS cc_start: 0.9318 (tmtt) cc_final: 0.9067 (tttp) REVERT: oA 152 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8793 (tmtt) REVERT: oA 156 LYS cc_start: 0.9344 (tmtt) cc_final: 0.9079 (tttp) REVERT: rA 304 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: rA 305 PHE cc_start: 0.8984 (t80) cc_final: 0.8614 (t80) REVERT: sA 355 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7114 (t80) REVERT: sA 356 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8718 (tttm) REVERT: uA 456 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9112 (tttp) REVERT: c 5 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8204 (t80) REVERT: 1A 56 LYS cc_start: 0.9371 (tmtt) cc_final: 0.9023 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8505 (tm-30) REVERT: 3A 153 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8625 (t80) REVERT: 4A 205 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8235 (t80) REVERT: 4A 206 LYS cc_start: 0.9190 (tttm) cc_final: 0.8764 (tttm) REVERT: 5A 256 LYS cc_start: 0.9225 (tmtt) cc_final: 0.8878 (tmtt) REVERT: 6A 302 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8865 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.9012 (tttm) REVERT: d 5 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8370 (t80) REVERT: HB 105 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8352 (t80) REVERT: JB 205 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8190 (t80) REVERT: JB 206 LYS cc_start: 0.9460 (tttm) cc_final: 0.9128 (tttm) REVERT: LB 302 LYS cc_start: 0.9234 (tmtt) cc_final: 0.8898 (ttmm) REVERT: LB 306 LYS cc_start: 0.9377 (tttm) cc_final: 0.9129 (tttm) REVERT: VB 52 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8444 (pptt) REVERT: XB 152 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8519 (pptt) REVERT: XB 157 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7618 (t80) REVERT: YB 204 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: YB 205 PHE cc_start: 0.8984 (t80) cc_final: 0.8596 (t80) REVERT: ZB 252 LYS cc_start: 0.9098 (tmtt) cc_final: 0.8450 (pptt) REVERT: aB 305 PHE cc_start: 0.9020 (t80) cc_final: 0.8736 (t80) REVERT: bB 352 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8338 (pptt) REVERT: dB 452 LYS cc_start: 0.9099 (tmtt) cc_final: 0.8418 (pptt) outliers start: 132 outliers final: 70 residues processed: 356 average time/residue: 0.3784 time to fit residues: 162.1650 Evaluate side-chains 447 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 322 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain U residue 404 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain TA residue 406 LYS Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 303 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain sA residue 356 LYS Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 153 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 302 LYS Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 402 LYS Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.153 8700 Z= 2.763 Angle : 2.725 20.629 11300 Z= 1.309 Chirality : 0.138 0.371 800 Planarity : 0.011 0.041 1500 Dihedral : 26.175 89.726 1021 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 117.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 22.50 % Allowed : 30.17 % Favored : 47.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.094 0.011 PHEaA 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 323 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: A 6 LYS cc_start: 0.9078 (tttt) cc_final: 0.8716 (tttm) REVERT: A 7 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: K 104 GLU cc_start: 0.8651 (mp0) cc_final: 0.8363 (mp0) REVERT: K 107 PHE cc_start: 0.9389 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: L 207 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8936 (m-80) REVERT: M 304 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: M 306 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8698 (tttt) REVERT: M 307 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.7998 (m-10) REVERT: B 4 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: U 404 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: C 4 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: C 6 LYS cc_start: 0.9181 (tttt) cc_final: 0.8819 (tttm) REVERT: Y 106 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8896 (ttmt) REVERT: k 104 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: m 304 GLU cc_start: 0.8652 (mp0) cc_final: 0.8424 (mp0) REVERT: E 4 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8294 (mp0) REVERT: E 6 LYS cc_start: 0.9005 (tttt) cc_final: 0.8725 (tttp) REVERT: r 104 GLU cc_start: 0.8696 (mp0) cc_final: 0.8421 (mp0) REVERT: u 404 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: u 406 LYS cc_start: 0.9027 (mptt) cc_final: 0.8633 (ttmt) REVERT: F 4 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7840 (tm-30) REVERT: F 7 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.8294 (m-10) REVERT: y 107 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: z 206 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8856 (ttpt) REVERT: z 207 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8185 (m-10) REVERT: 0 307 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: G 6 LYS cc_start: 0.9404 (tttt) cc_final: 0.8858 (tttm) REVERT: G 7 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: 6 206 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8840 (ttpt) REVERT: 6 207 PHE cc_start: 0.9249 (OUTLIER) cc_final: 0.8092 (m-10) REVERT: H 4 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: H 6 LYS cc_start: 0.9301 (tttt) cc_final: 0.8853 (ttmt) REVERT: EA 302 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8732 (ttmm) REVERT: JA 104 GLU cc_start: 0.4494 (OUTLIER) cc_final: 0.3838 (pm20) REVERT: LA 304 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8317 (pm20) REVERT: J 4 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: QA 104 GLU cc_start: 0.8870 (pm20) cc_final: 0.7506 (mm-30) REVERT: SA 304 GLU cc_start: 0.8904 (pm20) cc_final: 0.8525 (pm20) REVERT: TA 404 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7950 (tm-30) REVERT: a 3 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8473 (t80) REVERT: a 4 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: XA 52 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8751 (tmtt) REVERT: XA 55 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7857 (t80) REVERT: XA 56 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8933 (tttp) REVERT: YA 103 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8136 (t80) REVERT: YA 104 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: ZA 155 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8100 (t80) REVERT: ZA 156 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9137 (tttp) REVERT: aA 203 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8211 (t80) REVERT: bA 255 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7895 (t80) REVERT: cA 304 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8078 (tp30) REVERT: dA 355 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7645 (t80) REVERT: eA 403 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8526 (t80) REVERT: eA 404 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8061 (tm-30) REVERT: fA 455 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8137 (t80) REVERT: fA 456 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9115 (tttm) REVERT: mA 56 LYS cc_start: 0.9318 (tttt) cc_final: 0.9066 (tttp) REVERT: oA 156 LYS cc_start: 0.9360 (tmtt) cc_final: 0.9094 (tttp) REVERT: rA 304 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8131 (tp30) REVERT: rA 305 PHE cc_start: 0.8968 (t80) cc_final: 0.8645 (t80) REVERT: sA 355 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7084 (t80) REVERT: sA 356 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8741 (tttm) REVERT: uA 456 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9102 (tttp) REVERT: c 5 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8203 (t80) REVERT: 1A 56 LYS cc_start: 0.9383 (tmtt) cc_final: 0.9080 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8497 (tm-30) REVERT: 4A 205 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8228 (t80) REVERT: 4A 206 LYS cc_start: 0.9189 (tttm) cc_final: 0.8759 (tttm) REVERT: 5A 256 LYS cc_start: 0.9227 (tmtt) cc_final: 0.8879 (tmtt) REVERT: 6A 302 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8867 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8990 (tttm) REVERT: d 5 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8441 (t80) REVERT: HB 105 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8292 (t80) REVERT: JB 205 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8135 (t80) REVERT: JB 206 LYS cc_start: 0.9455 (tttm) cc_final: 0.9116 (tttm) REVERT: KB 256 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8843 (tmtt) REVERT: LB 302 LYS cc_start: 0.9232 (tmtt) cc_final: 0.8896 (ttmm) REVERT: LB 306 LYS cc_start: 0.9435 (tttm) cc_final: 0.9179 (tttm) REVERT: MB 356 LYS cc_start: 0.9060 (tmtt) cc_final: 0.8846 (tmtt) REVERT: VB 52 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8443 (pptt) REVERT: VB 56 LYS cc_start: 0.9447 (tmtt) cc_final: 0.9143 (tptp) REVERT: XB 152 LYS cc_start: 0.9074 (tmtt) cc_final: 0.8518 (pptt) REVERT: XB 157 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7616 (t80) REVERT: YB 204 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: YB 205 PHE cc_start: 0.8986 (t80) cc_final: 0.8600 (t80) REVERT: ZB 252 LYS cc_start: 0.9114 (tmtt) cc_final: 0.8476 (pptt) REVERT: aB 304 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: aB 305 PHE cc_start: 0.9027 (t80) cc_final: 0.8635 (t80) REVERT: bB 352 LYS cc_start: 0.9154 (tmtt) cc_final: 0.8354 (pptt) REVERT: dB 452 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8410 (pptt) outliers start: 135 outliers final: 70 residues processed: 359 average time/residue: 0.3588 time to fit residues: 153.6551 Evaluate side-chains 447 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 323 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain U residue 404 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 302 LYS Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain TA residue 406 LYS Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain fA residue 455 PHE Chi-restraints excluded: chain fA residue 456 LYS Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain sA residue 356 LYS Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 302 LYS Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 402 LYS Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.153 8700 Z= 2.765 Angle : 2.730 20.511 11300 Z= 1.311 Chirality : 0.138 0.388 800 Planarity : 0.011 0.041 1500 Dihedral : 26.139 89.626 1021 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 117.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Rotamer: Outliers : 21.67 % Allowed : 31.00 % Favored : 47.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.34), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.095 0.011 PHEaA 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 322 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8419 (mp0) REVERT: A 6 LYS cc_start: 0.9077 (tttt) cc_final: 0.8716 (tttm) REVERT: A 7 PHE cc_start: 0.9423 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: K 104 GLU cc_start: 0.8652 (mp0) cc_final: 0.8365 (mp0) REVERT: K 107 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8473 (m-80) REVERT: L 207 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.8961 (m-80) REVERT: M 304 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: M 306 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8698 (tttt) REVERT: M 307 PHE cc_start: 0.9414 (OUTLIER) cc_final: 0.7998 (m-10) REVERT: B 4 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: U 404 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: C 4 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8563 (mp0) REVERT: C 6 LYS cc_start: 0.9180 (tttt) cc_final: 0.8816 (tttm) REVERT: Y 106 LYS cc_start: 0.9190 (mtpt) cc_final: 0.8896 (ttmt) REVERT: k 104 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: m 304 GLU cc_start: 0.8692 (mp0) cc_final: 0.8457 (mp0) REVERT: E 4 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: E 6 LYS cc_start: 0.8999 (tttt) cc_final: 0.8721 (tttp) REVERT: r 104 GLU cc_start: 0.8700 (mp0) cc_final: 0.8423 (mp0) REVERT: u 404 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: u 406 LYS cc_start: 0.9035 (mptt) cc_final: 0.8653 (ttmt) REVERT: F 7 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8287 (m-10) REVERT: y 104 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: y 107 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: z 206 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8860 (ttpt) REVERT: z 207 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8164 (m-10) REVERT: 0 307 PHE cc_start: 0.9413 (OUTLIER) cc_final: 0.8654 (m-80) REVERT: G 6 LYS cc_start: 0.9404 (tttt) cc_final: 0.8863 (tttm) REVERT: G 7 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.7904 (m-10) REVERT: 6 206 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8846 (ttpt) REVERT: 6 207 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8093 (m-10) REVERT: H 4 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7828 (tm-30) REVERT: H 6 LYS cc_start: 0.9294 (tttt) cc_final: 0.8841 (tttp) REVERT: EA 302 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8730 (ttmm) REVERT: JA 104 GLU cc_start: 0.4534 (OUTLIER) cc_final: 0.3900 (pm20) REVERT: LA 304 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8316 (pm20) REVERT: J 4 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: QA 104 GLU cc_start: 0.8871 (pm20) cc_final: 0.7494 (mm-30) REVERT: SA 304 GLU cc_start: 0.8903 (pm20) cc_final: 0.8522 (pm20) REVERT: TA 404 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7951 (tm-30) REVERT: a 3 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8472 (t80) REVERT: a 4 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8054 (tp30) REVERT: a 6 LYS cc_start: 0.9305 (tttp) cc_final: 0.9088 (tttp) REVERT: XA 52 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8747 (tmtt) REVERT: XA 55 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7853 (t80) REVERT: XA 56 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8934 (tttp) REVERT: YA 103 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8148 (t80) REVERT: YA 104 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8044 (tp30) REVERT: ZA 155 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8097 (t80) REVERT: ZA 156 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9145 (tttp) REVERT: aA 203 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8134 (t80) REVERT: bA 255 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7897 (t80) REVERT: cA 304 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: dA 355 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7641 (t80) REVERT: eA 403 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8497 (t80) REVERT: eA 404 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8068 (tm-30) REVERT: mA 56 LYS cc_start: 0.9316 (tttt) cc_final: 0.9093 (tttp) REVERT: oA 156 LYS cc_start: 0.9364 (tmtt) cc_final: 0.9114 (tttp) REVERT: rA 304 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8122 (tp30) REVERT: rA 305 PHE cc_start: 0.8968 (t80) cc_final: 0.8645 (t80) REVERT: sA 355 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7322 (t80) REVERT: sA 356 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8736 (tttm) REVERT: uA 456 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9104 (tttp) REVERT: c 5 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8317 (t80) REVERT: 1A 56 LYS cc_start: 0.9381 (tmtt) cc_final: 0.9037 (tmtt) REVERT: 2A 104 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: 3A 154 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8286 (tm-30) REVERT: 4A 205 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8226 (t80) REVERT: 4A 206 LYS cc_start: 0.9190 (tttm) cc_final: 0.8729 (tttm) REVERT: 5A 256 LYS cc_start: 0.9237 (tmtt) cc_final: 0.8877 (tmtt) REVERT: 6A 302 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8868 (tmtt) REVERT: 7A 356 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8971 (tttm) REVERT: d 5 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.8379 (t80) REVERT: HB 105 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8357 (t80) REVERT: JB 205 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8208 (t80) REVERT: KB 256 LYS cc_start: 0.9125 (tmtt) cc_final: 0.8818 (tmtt) REVERT: LB 302 LYS cc_start: 0.9230 (tmtt) cc_final: 0.8895 (ttmm) REVERT: LB 306 LYS cc_start: 0.9368 (tttm) cc_final: 0.9127 (tttm) REVERT: MB 356 LYS cc_start: 0.9053 (tmtt) cc_final: 0.8808 (tmtt) REVERT: VB 52 LYS cc_start: 0.8994 (tmtt) cc_final: 0.8420 (pptt) REVERT: XB 152 LYS cc_start: 0.9076 (tmtt) cc_final: 0.8514 (pptt) REVERT: XB 157 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7602 (t80) REVERT: YB 204 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: YB 205 PHE cc_start: 0.8987 (t80) cc_final: 0.8602 (t80) REVERT: ZB 252 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8485 (pptt) REVERT: aB 304 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: aB 305 PHE cc_start: 0.9034 (t80) cc_final: 0.8625 (t80) REVERT: bB 352 LYS cc_start: 0.9144 (tmtt) cc_final: 0.8323 (pptt) REVERT: dB 452 LYS cc_start: 0.9125 (tmtt) cc_final: 0.8329 (pptt) outliers start: 130 outliers final: 70 residues processed: 359 average time/residue: 0.3651 time to fit residues: 156.4270 Evaluate side-chains 445 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 322 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain K residue 107 PHE Chi-restraints excluded: chain L residue 207 PHE Chi-restraints excluded: chain M residue 304 GLU Chi-restraints excluded: chain M residue 307 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain R residue 104 GLU Chi-restraints excluded: chain S residue 204 GLU Chi-restraints excluded: chain T residue 304 GLU Chi-restraints excluded: chain U residue 404 GLU Chi-restraints excluded: chain C residue 4 GLU Chi-restraints excluded: chain Y residue 104 GLU Chi-restraints excluded: chain Z residue 204 GLU Chi-restraints excluded: chain f residue 304 GLU Chi-restraints excluded: chain g residue 406 LYS Chi-restraints excluded: chain k residue 104 GLU Chi-restraints excluded: chain l residue 204 GLU Chi-restraints excluded: chain n residue 406 LYS Chi-restraints excluded: chain E residue 4 GLU Chi-restraints excluded: chain s residue 204 GLU Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 404 GLU Chi-restraints excluded: chain F residue 7 PHE Chi-restraints excluded: chain y residue 104 GLU Chi-restraints excluded: chain y residue 107 PHE Chi-restraints excluded: chain z residue 206 LYS Chi-restraints excluded: chain z residue 207 PHE Chi-restraints excluded: chain 0 residue 306 LYS Chi-restraints excluded: chain 0 residue 307 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain 6 residue 206 LYS Chi-restraints excluded: chain 6 residue 207 PHE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain CA residue 103 PHE Chi-restraints excluded: chain CA residue 104 GLU Chi-restraints excluded: chain DA residue 204 GLU Chi-restraints excluded: chain EA residue 302 LYS Chi-restraints excluded: chain EA residue 304 GLU Chi-restraints excluded: chain EA residue 306 LYS Chi-restraints excluded: chain FA residue 406 LYS Chi-restraints excluded: chain JA residue 104 GLU Chi-restraints excluded: chain JA residue 106 LYS Chi-restraints excluded: chain KA residue 206 LYS Chi-restraints excluded: chain J residue 4 GLU Chi-restraints excluded: chain TA residue 406 LYS Chi-restraints excluded: chain a residue 3 PHE Chi-restraints excluded: chain a residue 4 GLU Chi-restraints excluded: chain a residue 5 PHE Chi-restraints excluded: chain XA residue 55 PHE Chi-restraints excluded: chain XA residue 56 LYS Chi-restraints excluded: chain YA residue 102 LYS Chi-restraints excluded: chain YA residue 103 PHE Chi-restraints excluded: chain YA residue 104 GLU Chi-restraints excluded: chain YA residue 105 PHE Chi-restraints excluded: chain YA residue 106 LYS Chi-restraints excluded: chain ZA residue 155 PHE Chi-restraints excluded: chain ZA residue 156 LYS Chi-restraints excluded: chain aA residue 203 PHE Chi-restraints excluded: chain aA residue 205 PHE Chi-restraints excluded: chain bA residue 255 PHE Chi-restraints excluded: chain cA residue 304 GLU Chi-restraints excluded: chain dA residue 355 PHE Chi-restraints excluded: chain eA residue 403 PHE Chi-restraints excluded: chain eA residue 405 PHE Chi-restraints excluded: chain b residue 3 PHE Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain mA residue 55 PHE Chi-restraints excluded: chain nA residue 105 PHE Chi-restraints excluded: chain oA residue 155 PHE Chi-restraints excluded: chain qA residue 255 PHE Chi-restraints excluded: chain rA residue 304 GLU Chi-restraints excluded: chain sA residue 355 PHE Chi-restraints excluded: chain sA residue 356 LYS Chi-restraints excluded: chain tA residue 403 PHE Chi-restraints excluded: chain tA residue 405 PHE Chi-restraints excluded: chain uA residue 455 PHE Chi-restraints excluded: chain uA residue 456 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain c residue 5 PHE Chi-restraints excluded: chain 2A residue 103 PHE Chi-restraints excluded: chain 2A residue 104 GLU Chi-restraints excluded: chain 2A residue 105 PHE Chi-restraints excluded: chain 3A residue 155 PHE Chi-restraints excluded: chain 4A residue 203 PHE Chi-restraints excluded: chain 4A residue 205 PHE Chi-restraints excluded: chain 5A residue 255 PHE Chi-restraints excluded: chain 6A residue 302 LYS Chi-restraints excluded: chain 6A residue 303 PHE Chi-restraints excluded: chain 7A residue 355 PHE Chi-restraints excluded: chain 7A residue 356 LYS Chi-restraints excluded: chain 8A residue 403 PHE Chi-restraints excluded: chain 8A residue 405 PHE Chi-restraints excluded: chain d residue 3 PHE Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain HB residue 103 PHE Chi-restraints excluded: chain HB residue 105 PHE Chi-restraints excluded: chain HB residue 106 LYS Chi-restraints excluded: chain JB residue 205 PHE Chi-restraints excluded: chain KB residue 255 PHE Chi-restraints excluded: chain LB residue 303 PHE Chi-restraints excluded: chain MB residue 355 PHE Chi-restraints excluded: chain NB residue 403 PHE Chi-restraints excluded: chain NB residue 405 PHE Chi-restraints excluded: chain NB residue 406 LYS Chi-restraints excluded: chain e residue 3 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain VB residue 55 PHE Chi-restraints excluded: chain WB residue 103 PHE Chi-restraints excluded: chain WB residue 105 PHE Chi-restraints excluded: chain XB residue 155 PHE Chi-restraints excluded: chain XB residue 156 LYS Chi-restraints excluded: chain XB residue 157 PHE Chi-restraints excluded: chain YB residue 203 PHE Chi-restraints excluded: chain YB residue 204 GLU Chi-restraints excluded: chain ZB residue 255 PHE Chi-restraints excluded: chain aB residue 304 GLU Chi-restraints excluded: chain bB residue 355 PHE Chi-restraints excluded: chain cB residue 402 LYS Chi-restraints excluded: chain cB residue 403 PHE Chi-restraints excluded: chain cB residue 405 PHE Chi-restraints excluded: chain dB residue 455 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 5.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.078940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071660 restraints weight = 23357.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.073447 restraints weight = 8975.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.074608 restraints weight = 4580.873| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.6851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.153 8700 Z= 2.764 Angle : 2.732 20.495 11300 Z= 1.312 Chirality : 0.138 0.391 800 Planarity : 0.011 0.044 1500 Dihedral : 26.118 89.613 1021 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 118.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.50 % Favored : 75.50 % Rotamer: Outliers : 21.50 % Allowed : 31.50 % Favored : 47.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.33), residues: 400 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.101 0.011 PHEcA 303 =============================================================================== Job complete usr+sys time: 2263.96 seconds wall clock time: 41 minutes 14.77 seconds (2474.77 seconds total)