Starting phenix.real_space_refine on Mon Sep 23 21:12:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/09_2024/7lqf_23484.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/09_2024/7lqf_23484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/09_2024/7lqf_23484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/09_2024/7lqf_23484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/09_2024/7lqf_23484.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lqf_23484/09_2024/7lqf_23484.cif" } resolution = 3.8 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= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 3840 2.51 5 N 704 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5376 Number of models: 1 Model: "" Number of chains: 64 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: "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: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "X" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "j" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "k" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "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: "o" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "u" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "w" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "x" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "2" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "3" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "5" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: "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: "9" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "AA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "BA" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 84 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'5CR:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 3.52, per 1000 atoms: 0.65 Number of scatterers: 5376 At special positions: 0 Unit cell: (70.2, 87.48, 101.52, 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 832 8.00 N 704 7.00 C 3840 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: 1.31 Conformation dependent library (CDL) restraints added in 270.3 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 106 through 107 removed outlier: 6.813A pdb=" N LYS A 6 " --> pdb=" O PHE L 107 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS B 6 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS D 6 " --> pdb=" O PHE X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'k' and resid 305 through 306 removed outlier: 6.248A pdb=" N PHE j 205 " --> pdb=" O LYS k 306 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE W 305 " --> pdb=" O LYS j 206 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE V 205 " --> pdb=" O LYS W 306 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE Q 305 " --> pdb=" O LYS V 206 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE P 205 " --> pdb=" O LYS Q 306 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE K 305 " --> pdb=" O LYS P 206 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE J 205 " --> pdb=" O LYS K 306 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE M 205 " --> pdb=" O LYS N 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE S 205 " --> pdb=" O LYS T 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE Y 205 " --> pdb=" O LYS Z 306 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE m 205 " --> pdb=" O LYS n 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA4, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA6, first strand: chain 'a' and resid 4 through 6 removed outlier: 3.879A pdb=" N GLU a 4 " --> pdb=" O LYS r 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS r 106 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU r 104 " --> pdb=" O LYS a 6 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'o' and resid 104 through 106 removed outlier: 3.582A pdb=" N GLU o 104 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS o 106 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU c 4 " --> pdb=" O LYS o 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'y' and resid 202 through 205 removed outlier: 3.692A pdb=" N PHE z 305 " --> pdb=" O PHE y 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE y 205 " --> pdb=" O PHE z 303 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU s 204 " --> pdb=" O LYS z 306 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GMA z 308 " --> pdb=" O LYS s 202 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS s 202 " --> pdb=" O GMA z 308 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE t 305 " --> pdb=" O PHE s 203 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE s 205 " --> pdb=" O PHE t 303 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS p 206 " --> pdb=" O GLU t 304 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU p 204 " --> pdb=" O LYS t 306 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE q 305 " --> pdb=" O PHE p 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE p 205 " --> pdb=" O PHE q 303 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU v 204 " --> pdb=" O LYS q 306 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GMA q 308 " --> pdb=" O LYS v 202 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS v 202 " --> pdb=" O GMA q 308 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE w 305 " --> pdb=" O PHE v 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE v 205 " --> pdb=" O PHE w 303 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS 1 206 " --> pdb=" O GLU w 304 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU 1 204 " --> pdb=" O LYS w 306 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GMA w 308 " --> pdb=" O LYS 1 202 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS 1 202 " --> pdb=" O GMA w 308 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE 2 305 " --> pdb=" O PHE 1 203 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE 1 205 " --> pdb=" O PHE 2 303 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS 7 206 " --> pdb=" O GLU 2 304 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU 7 204 " --> pdb=" O LYS 2 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GMA 2 308 " --> pdb=" O LYS 7 202 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS 7 202 " --> pdb=" O GMA 2 308 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE 8 305 " --> pdb=" O PHE 7 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 7 205 " --> pdb=" O PHE 8 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 4 through 6 removed outlier: 3.815A pdb=" N GLU b 4 " --> pdb=" O LYS x 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'u' and resid 104 through 106 removed outlier: 3.578A pdb=" N GLU u 104 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS u 106 " --> pdb=" O GLU e 4 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU e 4 " --> pdb=" O LYS u 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 4 through 6 removed outlier: 3.865A pdb=" N GLU d 4 " --> pdb=" O LYS 3 106 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS 3 106 " --> pdb=" O GLU d 4 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU 3 104 " --> pdb=" O LYS d 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '0' and resid 104 through 106 removed outlier: 3.619A pdb=" N GLU 0 104 " --> pdb=" O LYS g 6 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS 0 106 " --> pdb=" O GLU g 4 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU g 4 " --> pdb=" O LYS 0 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 4 through 6 removed outlier: 3.795A pdb=" N GLU f 4 " --> pdb=" O LYS 9 106 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU 9 104 " --> pdb=" O LYS f 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 202 through 205 removed outlier: 3.693A pdb=" N PHE 5 305 " --> pdb=" O PHE 4 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 4 205 " --> pdb=" O PHE 5 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'AA' and resid 202 through 205 removed outlier: 3.692A pdb=" N PHEBA 305 " --> pdb=" O PHEAA 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHEAA 205 " --> pdb=" O PHEBA 303 " (cutoff:3.500A) 52 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 1.36 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: 649 1.25 - 1.33: 411 1.33 - 1.40: 1820 1.40 - 1.47: 576 1.47 - 1.54: 2112 Bond restraints: 5568 Sorted by residual: bond pdb=" N 5CR e 1 " pdb=" CAL 5CR e 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR a 1 " pdb=" CAL 5CR a 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " ideal model delta sigma weight residual 1.341 1.457 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" N 5CR b 1 " pdb=" CAL 5CR b 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" N 5CR f 1 " pdb=" CAL 5CR f 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 2.00e-02 2.50e+03 3.32e+01 ... (remaining 5563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 6235 1.90 - 3.80: 717 3.80 - 5.70: 192 5.70 - 7.60: 80 7.60 - 9.50: 8 Bond angle restraints: 7232 Sorted by residual: angle pdb=" C 5CR q 301 " pdb=" CA 5CR q 301 " pdb=" CB 5CR q 301 " ideal model delta sigma weight residual 110.10 116.12 -6.02 1.90e+00 2.77e-01 1.00e+01 angle pdb=" N 5CR g 1 " pdb=" CAL 5CR g 1 " pdb=" CAA 5CR g 1 " ideal model delta sigma weight residual 114.91 124.41 -9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C 5CR t 301 " pdb=" CA 5CR t 301 " pdb=" CB 5CR t 301 " ideal model delta sigma weight residual 110.10 116.11 -6.01 1.90e+00 2.77e-01 1.00e+01 angle pdb=" C 5CR 5 301 " pdb=" CA 5CR 5 301 " pdb=" CB 5CR 5 301 " ideal model delta sigma weight residual 110.10 116.10 -6.00 1.90e+00 2.77e-01 9.99e+00 angle pdb=" N 5CR d 1 " pdb=" CAL 5CR d 1 " pdb=" CAA 5CR d 1 " ideal model delta sigma weight residual 114.91 124.39 -9.48 3.00e+00 1.11e-01 9.99e+00 ... (remaining 7227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.80: 1977 10.80 - 21.61: 416 21.61 - 32.41: 159 32.41 - 43.21: 144 43.21 - 54.01: 56 Dihedral angle restraints: 2752 sinusoidal: 1280 harmonic: 1472 Sorted by residual: dihedral pdb=" CA LYS r 106 " pdb=" CB LYS r 106 " pdb=" CG LYS r 106 " pdb=" CD LYS r 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS 9 106 " pdb=" CB LYS 9 106 " pdb=" CG LYS 9 106 " pdb=" CD LYS 9 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.01 54.01 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA LYS u 106 " pdb=" CB LYS u 106 " pdb=" CG LYS u 106 " pdb=" CD LYS u 106 " ideal model delta sinusoidal sigma weight residual -60.00 -114.00 54.00 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.017: 172 0.017 - 0.034: 140 0.034 - 0.051: 124 0.051 - 0.067: 60 0.067 - 0.084: 16 Chirality restraints: 512 Sorted by residual: chirality pdb=" CA PHE j 203 " pdb=" N PHE j 203 " pdb=" C PHE j 203 " pdb=" CB PHE j 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.76e-01 chirality pdb=" CA PHE Y 203 " pdb=" N PHE Y 203 " pdb=" C PHE Y 203 " pdb=" CB PHE Y 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.73e-01 chirality pdb=" CA PHE m 203 " pdb=" N PHE m 203 " pdb=" C PHE m 203 " pdb=" CB PHE m 203 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.71e-01 ... (remaining 509 not shown) Planarity restraints: 960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE p 203 " 0.009 2.00e-02 2.50e+03 6.10e-03 6.51e-01 pdb=" CG PHE p 203 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE p 203 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE p 203 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE p 203 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE p 203 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE p 203 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEBA 303 " 0.005 2.00e-02 2.50e+03 5.92e-03 6.14e-01 pdb=" CG PHEBA 303 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHEBA 303 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEBA 303 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHEBA 303 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHEBA 303 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHEBA 303 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 4 203 " -0.009 2.00e-02 2.50e+03 5.91e-03 6.11e-01 pdb=" CG PHE 4 203 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE 4 203 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE 4 203 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE 4 203 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE 4 203 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE 4 203 " -0.004 2.00e-02 2.50e+03 ... (remaining 957 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1729 2.79 - 3.31: 4534 3.31 - 3.84: 8714 3.84 - 4.37: 11165 4.37 - 4.90: 19430 Nonbonded interactions: 45572 Sorted by model distance: nonbonded pdb=" O GMA I 108 " pdb=" N 5CR J 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA i 108 " pdb=" N 5CR j 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA X 108 " pdb=" N 5CR Y 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA l 108 " pdb=" N 5CR m 201 " model vdw 2.258 3.120 nonbonded pdb=" O GMA R 108 " pdb=" N 5CR S 201 " model vdw 2.258 3.120 ... (remaining 45567 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.780 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 0.116 5568 Z= 0.863 Angle : 1.461 9.501 7232 Z= 0.602 Chirality : 0.035 0.084 512 Planarity : 0.002 0.007 960 Dihedral : 18.365 54.014 1728 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % 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: -4.77 (0.32), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.24), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9136 (tttt) cc_final: 0.8811 (tptm) REVERT: A 7 PHE cc_start: 0.8216 (m-10) cc_final: 0.7886 (m-10) REVERT: J 202 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7898 (ttmm) REVERT: K 306 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7586 (mmmm) REVERT: B 2 LYS cc_start: 0.9157 (tttt) cc_final: 0.8892 (tptm) REVERT: B 6 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7432 (mmmm) REVERT: L 102 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8600 (mmtt) REVERT: M 204 GLU cc_start: 0.8113 (pt0) cc_final: 0.7204 (pm20) REVERT: N 306 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7691 (mmmm) REVERT: Q 306 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7608 (mmmm) REVERT: D 2 LYS cc_start: 0.9124 (tttt) cc_final: 0.8722 (tptm) REVERT: D 3 PHE cc_start: 0.8401 (m-80) cc_final: 0.8172 (m-80) REVERT: D 6 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7546 (mmmm) REVERT: R 104 GLU cc_start: 0.7921 (tm-30) cc_final: 0.6923 (tm-30) REVERT: S 204 GLU cc_start: 0.8108 (pt0) cc_final: 0.7535 (pm20) REVERT: T 305 PHE cc_start: 0.8456 (m-80) cc_final: 0.8254 (m-10) REVERT: T 306 LYS cc_start: 0.8181 (mmmm) cc_final: 0.7671 (mmmm) REVERT: E 2 LYS cc_start: 0.9014 (tttt) cc_final: 0.8717 (tptm) REVERT: U 104 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7072 (tm-30) REVERT: V 204 GLU cc_start: 0.8325 (pt0) cc_final: 0.7746 (pm20) REVERT: W 302 LYS cc_start: 0.8301 (tppp) cc_final: 0.7719 (tppp) REVERT: W 306 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7862 (mmmm) REVERT: F 2 LYS cc_start: 0.9090 (tttt) cc_final: 0.8422 (tmtt) REVERT: X 104 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7017 (tm-30) REVERT: X 106 LYS cc_start: 0.7894 (tppt) cc_final: 0.7561 (tppt) REVERT: Y 204 GLU cc_start: 0.8371 (pt0) cc_final: 0.7350 (pp20) REVERT: Z 306 LYS cc_start: 0.8050 (mmmm) cc_final: 0.7335 (mmmm) REVERT: G 6 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7868 (ttmm) REVERT: i 102 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8357 (mmtt) REVERT: i 104 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7020 (tm-30) REVERT: i 106 LYS cc_start: 0.7678 (tppt) cc_final: 0.7407 (tppt) REVERT: j 204 GLU cc_start: 0.8071 (pt0) cc_final: 0.7744 (pm20) REVERT: k 304 GLU cc_start: 0.7250 (tm-30) cc_final: 0.6755 (tm-30) REVERT: H 3 PHE cc_start: 0.8404 (m-80) cc_final: 0.8026 (m-80) REVERT: l 102 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8558 (mmtt) REVERT: m 204 GLU cc_start: 0.7905 (pt0) cc_final: 0.7370 (pm20) REVERT: m 205 PHE cc_start: 0.8286 (m-80) cc_final: 0.8052 (m-80) REVERT: n 306 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7577 (mmmm) REVERT: p 203 PHE cc_start: 0.7511 (t80) cc_final: 0.7309 (t80) REVERT: q 303 PHE cc_start: 0.8252 (t80) cc_final: 0.7808 (t80) REVERT: q 307 PHE cc_start: 0.7542 (t80) cc_final: 0.7293 (t80) REVERT: r 105 PHE cc_start: 0.9015 (p90) cc_final: 0.8791 (p90) REVERT: t 303 PHE cc_start: 0.8188 (t80) cc_final: 0.7770 (t80) REVERT: t 305 PHE cc_start: 0.7586 (t80) cc_final: 0.7183 (t80) REVERT: v 204 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7051 (tm-30) REVERT: w 302 LYS cc_start: 0.8898 (tmtt) cc_final: 0.8490 (tmtt) REVERT: x 105 PHE cc_start: 0.8978 (p90) cc_final: 0.8358 (p90) REVERT: x 107 PHE cc_start: 0.8027 (t80) cc_final: 0.7191 (t80) REVERT: z 305 PHE cc_start: 0.7904 (t80) cc_final: 0.7476 (t80) REVERT: e 6 LYS cc_start: 0.8611 (ttmt) cc_final: 0.8167 (ttmm) REVERT: e 7 PHE cc_start: 0.9053 (t80) cc_final: 0.8752 (t80) REVERT: 1 202 LYS cc_start: 0.8057 (tptp) cc_final: 0.7783 (tptp) REVERT: 2 305 PHE cc_start: 0.7995 (t80) cc_final: 0.7673 (t80) REVERT: f 7 PHE cc_start: 0.8908 (t80) cc_final: 0.8382 (t80) REVERT: 3 105 PHE cc_start: 0.8867 (p90) cc_final: 0.8660 (p90) REVERT: 3 106 LYS cc_start: 0.8748 (tmtt) cc_final: 0.8356 (ttpp) REVERT: 4 204 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7088 (tm-30) REVERT: 5 303 PHE cc_start: 0.8146 (t80) cc_final: 0.7910 (t80) REVERT: g 2 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8492 (mmtt) REVERT: 6 106 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8435 (ttpp) REVERT: 7 204 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7069 (tm-30) REVERT: 8 302 LYS cc_start: 0.8846 (tmtt) cc_final: 0.8593 (tmtt) REVERT: 8 307 PHE cc_start: 0.7753 (t80) cc_final: 0.7394 (t80) REVERT: 9 107 PHE cc_start: 0.7939 (t80) cc_final: 0.7557 (t80) outliers start: 8 outliers final: 0 residues processed: 164 average time/residue: 0.3612 time to fit residues: 67.0194 Evaluate side-chains 161 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain G residue 6 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.6980 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: 0.8356 moved from start: 0.8815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.153 0.471 5568 Z= 8.411 Angle : 6.008 58.256 7232 Z= 2.679 Chirality : 0.409 1.111 512 Planarity : 0.029 0.097 960 Dihedral : 25.177 84.646 652 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 194.90 Ramachandran Plot: Outliers : 7.42 % Allowed : 33.59 % Favored : 58.98 % Rotamer: Outliers : 15.89 % Allowed : 27.08 % Favored : 57.03 % Cbeta Deviations : 47.85 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.79 % 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: -8.46 (0.26), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.44 (0.20), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.199 0.029 PHE 3 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 169 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8665 (ttmm) REVERT: A 7 PHE cc_start: 0.9179 (OUTLIER) cc_final: 0.8949 (m-10) REVERT: I 107 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8408 (m-10) REVERT: J 206 LYS cc_start: 0.9000 (tttm) cc_final: 0.7696 (ttpp) REVERT: K 302 LYS cc_start: 0.8995 (tppp) cc_final: 0.8749 (tppp) REVERT: K 306 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8194 (mmmm) REVERT: M 202 LYS cc_start: 0.9274 (ttmm) cc_final: 0.8966 (ttmm) REVERT: M 206 LYS cc_start: 0.8755 (tttm) cc_final: 0.8030 (tttm) REVERT: N 302 LYS cc_start: 0.8832 (tppp) cc_final: 0.8554 (tppp) REVERT: N 304 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7861 (tm-30) REVERT: N 306 LYS cc_start: 0.8722 (mmmm) cc_final: 0.7999 (mmmm) REVERT: N 307 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8286 (t80) REVERT: Q 303 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: S 202 LYS cc_start: 0.9325 (ttmm) cc_final: 0.8894 (ttpp) REVERT: S 206 LYS cc_start: 0.8933 (tttm) cc_final: 0.7626 (ttpp) REVERT: T 306 LYS cc_start: 0.8611 (mmmm) cc_final: 0.7967 (mmmm) REVERT: E 6 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8592 (ttmm) REVERT: U 103 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: W 304 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7189 (tm-30) REVERT: W 306 LYS cc_start: 0.8816 (mmmm) cc_final: 0.8118 (mmmm) REVERT: Y 206 LYS cc_start: 0.8661 (tttm) cc_final: 0.8196 (tttm) REVERT: Z 304 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8101 (tm-30) REVERT: Z 306 LYS cc_start: 0.8503 (mmmm) cc_final: 0.7951 (mmmm) REVERT: Z 307 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7627 (m-80) REVERT: G 2 LYS cc_start: 0.9298 (tptt) cc_final: 0.8956 (tptm) REVERT: G 6 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8231 (ttmm) REVERT: G 7 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: i 102 LYS cc_start: 0.8974 (mmtt) cc_final: 0.8749 (mmmt) REVERT: i 106 LYS cc_start: 0.4588 (tppt) cc_final: 0.4014 (tptt) REVERT: i 107 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8537 (m-10) REVERT: H 6 LYS cc_start: 0.9317 (mmmm) cc_final: 0.9106 (mmmm) REVERT: l 103 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: l 106 LYS cc_start: 0.8948 (tppt) cc_final: 0.8494 (tppt) REVERT: m 202 LYS cc_start: 0.9234 (ttmm) cc_final: 0.8833 (ttmm) REVERT: m 204 GLU cc_start: 0.8960 (pt0) cc_final: 0.8547 (pt0) REVERT: n 302 LYS cc_start: 0.8943 (tppp) cc_final: 0.8664 (tppp) REVERT: n 304 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7840 (tm-30) REVERT: n 306 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8258 (mmmm) REVERT: n 307 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8725 (t80) REVERT: a 2 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8398 (mmtt) REVERT: o 102 LYS cc_start: 0.9045 (tptp) cc_final: 0.8792 (tptp) REVERT: p 204 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7936 (tm-30) REVERT: r 104 GLU cc_start: 0.8872 (pp20) cc_final: 0.8568 (pp20) REVERT: s 206 LYS cc_start: 0.8691 (tptp) cc_final: 0.8245 (tptp) REVERT: t 306 LYS cc_start: 0.9080 (tmtt) cc_final: 0.8158 (tmtt) REVERT: c 2 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8697 (mmtt) REVERT: u 104 GLU cc_start: 0.8782 (pp20) cc_final: 0.8459 (pp20) REVERT: v 204 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7709 (tm-30) REVERT: d 7 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8877 (t80) REVERT: y 204 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7460 (tm-30) REVERT: z 306 LYS cc_start: 0.8914 (tttt) cc_final: 0.7893 (tmtt) REVERT: z 307 PHE cc_start: 0.8870 (t80) cc_final: 0.8650 (t80) REVERT: 0 106 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8693 (ttpp) REVERT: 2 302 LYS cc_start: 0.9238 (tmtt) cc_final: 0.8690 (tmtt) REVERT: 3 102 LYS cc_start: 0.9116 (tptp) cc_final: 0.8788 (tptp) REVERT: 3 103 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8104 (p90) REVERT: 3 107 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8412 (t80) REVERT: 4 204 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7868 (tm-30) REVERT: 5 307 PHE cc_start: 0.8827 (t80) cc_final: 0.8594 (t80) REVERT: g 2 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8497 (mmtt) REVERT: 6 102 LYS cc_start: 0.9094 (tptp) cc_final: 0.8856 (tptp) REVERT: 7 202 LYS cc_start: 0.9089 (tptp) cc_final: 0.8724 (tptp) REVERT: 7 204 GLU cc_start: 0.8448 (tm-30) cc_final: 0.7729 (tm-30) REVERT: 8 306 LYS cc_start: 0.8636 (tttt) cc_final: 0.7892 (tmtt) REVERT: 8 307 PHE cc_start: 0.8691 (t80) cc_final: 0.8373 (t80) REVERT: AA 206 LYS cc_start: 0.8810 (tptp) cc_final: 0.8392 (tptp) REVERT: BA 307 PHE cc_start: 0.8835 (t80) cc_final: 0.8550 (t80) outliers start: 61 outliers final: 29 residues processed: 210 average time/residue: 0.3588 time to fit residues: 85.2293 Evaluate side-chains 206 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 162 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 107 PHE Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain d residue 7 PHE Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 106 LYS Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.9520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.554 5568 Z= 8.462 Angle : 6.140 59.280 7232 Z= 2.734 Chirality : 0.415 1.070 512 Planarity : 0.028 0.090 960 Dihedral : 25.378 89.349 648 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 194.01 Ramachandran Plot: Outliers : 3.12 % Allowed : 53.91 % Favored : 42.97 % Rotamer: Outliers : 20.83 % Allowed : 30.47 % Favored : 48.70 % Cbeta Deviations : 45.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.90 % 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: -9.08 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.92 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.186 0.027 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 161 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9335 (tptt) cc_final: 0.9019 (tptt) REVERT: A 5 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8086 (m-10) REVERT: A 7 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8886 (m-10) REVERT: I 107 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.8511 (m-10) REVERT: J 206 LYS cc_start: 0.9002 (tttm) cc_final: 0.8321 (ttpp) REVERT: K 302 LYS cc_start: 0.9017 (tppp) cc_final: 0.8760 (tppp) REVERT: K 306 LYS cc_start: 0.8711 (mmmm) cc_final: 0.8183 (mmmm) REVERT: M 202 LYS cc_start: 0.9237 (ttmm) cc_final: 0.8919 (ttmm) REVERT: N 302 LYS cc_start: 0.8985 (tppp) cc_final: 0.8768 (tppp) REVERT: N 304 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7875 (tm-30) REVERT: N 306 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8129 (mmmm) REVERT: N 307 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8143 (t80) REVERT: P 202 LYS cc_start: 0.9218 (ttmm) cc_final: 0.8957 (ttmm) REVERT: P 206 LYS cc_start: 0.8663 (tttm) cc_final: 0.8276 (tttm) REVERT: Q 302 LYS cc_start: 0.8801 (tppp) cc_final: 0.8508 (mmmm) REVERT: S 202 LYS cc_start: 0.9235 (ttmm) cc_final: 0.8065 (ttpp) REVERT: S 206 LYS cc_start: 0.8902 (tttm) cc_final: 0.7776 (ttpp) REVERT: T 304 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7873 (tm-30) REVERT: E 6 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8704 (ttmm) REVERT: U 103 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: W 302 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8400 (ttpp) REVERT: W 304 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7136 (tm-30) REVERT: X 103 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8692 (m-10) REVERT: Y 206 LYS cc_start: 0.8617 (tttm) cc_final: 0.8259 (tttm) REVERT: Z 302 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8202 (tppp) REVERT: Z 304 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8202 (tm-30) REVERT: Z 306 LYS cc_start: 0.8573 (mmmm) cc_final: 0.8008 (mmmm) REVERT: Z 307 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: G 5 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: G 6 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8458 (ttmm) REVERT: G 7 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: i 102 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8715 (mmmt) REVERT: i 103 PHE cc_start: 0.9229 (OUTLIER) cc_final: 0.8898 (m-10) REVERT: j 206 LYS cc_start: 0.8860 (tttm) cc_final: 0.8321 (ttpp) REVERT: k 304 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7186 (tm-30) REVERT: H 6 LYS cc_start: 0.9288 (mmmm) cc_final: 0.9049 (mmmm) REVERT: l 102 LYS cc_start: 0.9415 (mmtt) cc_final: 0.9101 (mmtt) REVERT: l 103 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: m 202 LYS cc_start: 0.9295 (ttmm) cc_final: 0.8961 (ttmm) REVERT: m 204 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8549 (pt0) REVERT: m 206 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8129 (pttm) REVERT: n 302 LYS cc_start: 0.8908 (tppp) cc_final: 0.8618 (tppp) REVERT: n 304 GLU cc_start: 0.8538 (tm-30) cc_final: 0.7903 (tm-30) REVERT: n 306 LYS cc_start: 0.8820 (mmmm) cc_final: 0.8365 (mmmm) REVERT: n 307 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8678 (t80) REVERT: a 2 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8362 (mmtt) REVERT: q 306 LYS cc_start: 0.9003 (tttt) cc_final: 0.8616 (tttp) REVERT: q 307 PHE cc_start: 0.8711 (t80) cc_final: 0.8070 (t80) REVERT: b 2 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8781 (mmtt) REVERT: s 202 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8745 (tppp) REVERT: t 303 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.7217 (t80) REVERT: c 2 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8698 (mmtt) REVERT: u 104 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8270 (pp20) REVERT: v 204 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7773 (tm-30) REVERT: v 207 PHE cc_start: 0.8769 (t80) cc_final: 0.7755 (t80) REVERT: x 104 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8652 (pp20) REVERT: y 202 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8547 (ttmm) REVERT: y 204 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7664 (tm-30) REVERT: z 302 LYS cc_start: 0.8974 (tmtt) cc_final: 0.8502 (tmtt) REVERT: 1 203 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8262 (t80) REVERT: 2 302 LYS cc_start: 0.9169 (tmtt) cc_final: 0.8624 (tmtt) REVERT: 3 102 LYS cc_start: 0.9144 (tptp) cc_final: 0.8796 (tptp) REVERT: 3 103 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8377 (p90) REVERT: 3 107 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8466 (t80) REVERT: 4 206 LYS cc_start: 0.8850 (tptp) cc_final: 0.8618 (tptp) REVERT: 5 306 LYS cc_start: 0.8811 (tttt) cc_final: 0.8408 (tttp) REVERT: g 2 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8460 (mmtt) REVERT: 7 204 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7852 (tm-30) REVERT: 8 307 PHE cc_start: 0.8592 (t80) cc_final: 0.8263 (t80) REVERT: h 2 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8693 (mmtt) REVERT: AA 206 LYS cc_start: 0.8708 (tptp) cc_final: 0.8299 (tptp) REVERT: BA 302 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8687 (tmtt) REVERT: BA 307 PHE cc_start: 0.8817 (t80) cc_final: 0.8498 (t80) outliers start: 80 outliers final: 39 residues processed: 213 average time/residue: 0.3613 time to fit residues: 87.1631 Evaluate side-chains 224 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 161 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain p residue 205 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 103 PHE Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.9723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.489 5568 Z= 8.444 Angle : 6.183 59.492 7232 Z= 2.750 Chirality : 0.414 1.043 512 Planarity : 0.028 0.091 960 Dihedral : 25.116 89.703 644 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 194.45 Ramachandran Plot: Outliers : 1.95 % Allowed : 55.86 % Favored : 42.19 % Rotamer: Outliers : 24.74 % Allowed : 33.07 % Favored : 42.19 % Cbeta Deviations : 45.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.01 % 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: -9.08 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.91 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.026 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 162 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.8082 (m-10) REVERT: A 7 PHE cc_start: 0.9159 (OUTLIER) cc_final: 0.8924 (m-10) REVERT: I 107 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8532 (m-10) REVERT: J 206 LYS cc_start: 0.8973 (tttm) cc_final: 0.8379 (ttpp) REVERT: K 302 LYS cc_start: 0.9068 (tppp) cc_final: 0.8686 (tppp) REVERT: K 306 LYS cc_start: 0.8682 (mmmm) cc_final: 0.8221 (mmmm) REVERT: L 103 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: M 202 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8913 (ttmm) REVERT: M 206 LYS cc_start: 0.8817 (tttm) cc_final: 0.8486 (tttm) REVERT: N 302 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8745 (tppp) REVERT: N 304 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7991 (tm-30) REVERT: N 306 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8090 (mmmm) REVERT: N 307 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8228 (t80) REVERT: Q 302 LYS cc_start: 0.8846 (tppp) cc_final: 0.8521 (mmmm) REVERT: Q 303 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7363 (m-80) REVERT: Q 306 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7984 (mmmm) REVERT: Q 307 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.7911 (t80) REVERT: S 202 LYS cc_start: 0.9309 (ttmm) cc_final: 0.8070 (ttpp) REVERT: S 206 LYS cc_start: 0.8880 (tttm) cc_final: 0.8445 (ttpp) REVERT: T 304 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7381 (tm-30) REVERT: T 306 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8099 (mmtp) REVERT: E 6 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8755 (ttmm) REVERT: U 103 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: U 106 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8362 (tppt) REVERT: V 206 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.7952 (ttpp) REVERT: W 302 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8694 (ttpp) REVERT: W 304 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7067 (tm-30) REVERT: Y 206 LYS cc_start: 0.8666 (tttm) cc_final: 0.8340 (tttm) REVERT: Z 302 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8228 (tppp) REVERT: Z 307 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: G 5 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8047 (m-80) REVERT: G 6 LYS cc_start: 0.8780 (ttmm) cc_final: 0.7906 (ttmm) REVERT: G 7 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: i 102 LYS cc_start: 0.8996 (mmtt) cc_final: 0.8715 (mmmt) REVERT: i 103 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8801 (m-10) REVERT: H 6 LYS cc_start: 0.9297 (mmmm) cc_final: 0.9026 (mmmm) REVERT: l 102 LYS cc_start: 0.9394 (mmtt) cc_final: 0.9137 (mmtm) REVERT: l 103 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: m 202 LYS cc_start: 0.9297 (ttmm) cc_final: 0.9013 (ttmm) REVERT: m 204 GLU cc_start: 0.9005 (pt0) cc_final: 0.8635 (pt0) REVERT: m 206 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8241 (pttm) REVERT: n 302 LYS cc_start: 0.8923 (tppp) cc_final: 0.8650 (tppp) REVERT: n 304 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7901 (tm-30) REVERT: n 306 LYS cc_start: 0.8776 (mmmm) cc_final: 0.8340 (mmmm) REVERT: n 307 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8641 (t80) REVERT: a 2 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8351 (mmtt) REVERT: o 107 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8145 (t80) REVERT: q 303 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7439 (t80) REVERT: q 306 LYS cc_start: 0.9031 (tttt) cc_final: 0.8652 (tttp) REVERT: q 307 PHE cc_start: 0.8705 (t80) cc_final: 0.8103 (t80) REVERT: b 2 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8555 (mmtt) REVERT: s 204 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8106 (tm-30) REVERT: t 303 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7194 (t80) REVERT: c 2 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8745 (mmtt) REVERT: u 104 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: v 204 GLU cc_start: 0.8595 (tm-30) cc_final: 0.7789 (tm-30) REVERT: v 207 PHE cc_start: 0.8800 (t80) cc_final: 0.7729 (t80) REVERT: x 104 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8520 (pp20) REVERT: y 202 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8690 (ttmm) REVERT: y 203 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8317 (t80) REVERT: z 302 LYS cc_start: 0.8979 (tmtt) cc_final: 0.8466 (tmtt) REVERT: 1 203 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.8214 (t80) REVERT: 2 306 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8366 (tmtt) REVERT: f 2 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8423 (mmtt) REVERT: 3 102 LYS cc_start: 0.9073 (tptp) cc_final: 0.8769 (tptp) REVERT: 4 206 LYS cc_start: 0.8786 (tptp) cc_final: 0.8468 (tptp) REVERT: 5 306 LYS cc_start: 0.8835 (tttp) cc_final: 0.8394 (tttt) REVERT: 5 307 PHE cc_start: 0.8986 (t80) cc_final: 0.8694 (t80) REVERT: g 2 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8402 (mmtt) REVERT: 8 302 LYS cc_start: 0.9056 (tmtt) cc_final: 0.8629 (tmtt) REVERT: 8 307 PHE cc_start: 0.8608 (t80) cc_final: 0.8319 (t80) REVERT: 9 102 LYS cc_start: 0.9070 (tptp) cc_final: 0.8846 (tptp) REVERT: 9 104 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7657 (tm-30) REVERT: AA 206 LYS cc_start: 0.8724 (tptp) cc_final: 0.8395 (tptp) REVERT: BA 302 LYS cc_start: 0.8977 (tmtt) cc_final: 0.8681 (tmtt) REVERT: BA 307 PHE cc_start: 0.8892 (t80) cc_final: 0.8504 (t80) outliers start: 95 outliers final: 48 residues processed: 218 average time/residue: 0.3525 time to fit residues: 86.9659 Evaluate side-chains 240 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 162 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain n residue 307 PHE Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain r residue 103 PHE Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 3 residue 107 PHE Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.9936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.476 5568 Z= 8.466 Angle : 6.233 58.780 7232 Z= 2.764 Chirality : 0.416 1.048 512 Planarity : 0.028 0.091 960 Dihedral : 25.454 89.710 640 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 197.19 Ramachandran Plot: Outliers : 2.34 % Allowed : 56.64 % Favored : 41.02 % Rotamer: Outliers : 25.78 % Allowed : 32.29 % Favored : 41.93 % Cbeta Deviations : 46.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.68 % 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: -9.14 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.96 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.026 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 162 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8069 (m-10) REVERT: A 7 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8899 (m-10) REVERT: I 102 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8848 (mmtm) REVERT: I 107 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.8525 (m-10) REVERT: J 206 LYS cc_start: 0.8941 (tttm) cc_final: 0.8424 (ttpp) REVERT: K 302 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8663 (tppp) REVERT: K 306 LYS cc_start: 0.8672 (mmmm) cc_final: 0.8147 (mmmm) REVERT: L 103 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: M 202 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8916 (ttmm) REVERT: M 206 LYS cc_start: 0.8782 (tttm) cc_final: 0.8411 (tttm) REVERT: N 302 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8747 (tppp) REVERT: N 304 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8015 (tm-30) REVERT: N 306 LYS cc_start: 0.8681 (mmmm) cc_final: 0.8100 (mmmm) REVERT: N 307 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8209 (t80) REVERT: Q 302 LYS cc_start: 0.8767 (tppp) cc_final: 0.8499 (tppp) REVERT: Q 303 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: Q 307 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8297 (t80) REVERT: S 202 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8036 (ttpp) REVERT: S 206 LYS cc_start: 0.8736 (tttm) cc_final: 0.7781 (ttpp) REVERT: T 304 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7363 (tm-30) REVERT: T 306 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8100 (mmtp) REVERT: E 6 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8838 (ttmm) REVERT: U 103 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: U 106 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8411 (tppt) REVERT: V 206 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8546 (ttpp) REVERT: W 302 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8444 (ttpp) REVERT: W 304 GLU cc_start: 0.8154 (tm-30) cc_final: 0.6796 (tm-30) REVERT: W 306 LYS cc_start: 0.8677 (mmmm) cc_final: 0.7944 (mmtm) REVERT: F 5 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8266 (m-80) REVERT: X 103 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8691 (m-10) REVERT: Y 206 LYS cc_start: 0.8656 (tttm) cc_final: 0.8390 (tttm) REVERT: Z 302 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8100 (tppp) REVERT: Z 304 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7984 (tm-30) REVERT: Z 306 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8042 (mmmm) REVERT: Z 307 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: G 5 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: G 7 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: i 102 LYS cc_start: 0.9000 (mmtt) cc_final: 0.8696 (mmmt) REVERT: i 103 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8801 (m-80) REVERT: j 202 LYS cc_start: 0.9245 (ttmm) cc_final: 0.8883 (ttmm) REVERT: H 6 LYS cc_start: 0.9276 (mmmm) cc_final: 0.8990 (mmmm) REVERT: l 102 LYS cc_start: 0.9424 (mmtt) cc_final: 0.9200 (mmtm) REVERT: l 103 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: n 302 LYS cc_start: 0.8942 (tppp) cc_final: 0.8727 (tppp) REVERT: n 304 GLU cc_start: 0.8545 (tm-30) cc_final: 0.7960 (tm-30) REVERT: n 306 LYS cc_start: 0.8772 (mmmm) cc_final: 0.8496 (mmmm) REVERT: a 2 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8349 (mmtt) REVERT: o 107 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8155 (t80) REVERT: p 203 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8176 (t80) REVERT: q 302 LYS cc_start: 0.9186 (tmtt) cc_final: 0.8731 (tmtt) REVERT: q 303 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.7147 (t80) REVERT: q 305 PHE cc_start: 0.9038 (t80) cc_final: 0.8763 (t80) REVERT: q 306 LYS cc_start: 0.9025 (tttt) cc_final: 0.8576 (tttp) REVERT: q 307 PHE cc_start: 0.8696 (t80) cc_final: 0.7972 (t80) REVERT: b 2 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8529 (mmtt) REVERT: s 202 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8768 (tppp) REVERT: s 204 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8113 (tm-30) REVERT: t 303 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.7314 (t80) REVERT: c 2 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8681 (mmtt) REVERT: v 204 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7778 (tm-30) REVERT: v 207 PHE cc_start: 0.8793 (t80) cc_final: 0.7717 (t80) REVERT: x 104 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8594 (pp20) REVERT: y 203 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8319 (t80) REVERT: z 302 LYS cc_start: 0.8978 (tmtt) cc_final: 0.8468 (tmtt) REVERT: 1 203 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8266 (t80) REVERT: 2 306 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8376 (tmtt) REVERT: f 2 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8352 (mmtt) REVERT: 3 102 LYS cc_start: 0.9100 (tptp) cc_final: 0.8787 (tptp) REVERT: 4 202 LYS cc_start: 0.9092 (tptp) cc_final: 0.8705 (tppp) REVERT: 4 206 LYS cc_start: 0.8723 (tptp) cc_final: 0.8439 (tptp) REVERT: 5 306 LYS cc_start: 0.8880 (tttp) cc_final: 0.8330 (tttp) REVERT: 5 307 PHE cc_start: 0.8939 (t80) cc_final: 0.8662 (t80) REVERT: g 2 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8411 (mmtt) REVERT: 6 102 LYS cc_start: 0.9013 (tptp) cc_final: 0.8795 (tptp) REVERT: 7 202 LYS cc_start: 0.9090 (tptp) cc_final: 0.8629 (tptp) REVERT: 7 203 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8119 (t80) REVERT: 8 307 PHE cc_start: 0.8547 (t80) cc_final: 0.8284 (t80) REVERT: 9 102 LYS cc_start: 0.9050 (tptp) cc_final: 0.8693 (tptp) REVERT: 9 104 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7800 (tm-30) REVERT: AA 206 LYS cc_start: 0.8724 (tptp) cc_final: 0.8423 (tptp) REVERT: BA 302 LYS cc_start: 0.9037 (tmtt) cc_final: 0.8812 (tmtt) REVERT: BA 307 PHE cc_start: 0.8875 (t80) cc_final: 0.8430 (t80) outliers start: 99 outliers final: 53 residues processed: 222 average time/residue: 0.3711 time to fit residues: 93.4688 Evaluate side-chains 247 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 160 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain G residue 7 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain p residue 205 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 0 residue 104 GLU Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.9972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.473 5568 Z= 8.458 Angle : 6.202 58.540 7232 Z= 2.752 Chirality : 0.416 1.096 512 Planarity : 0.028 0.093 960 Dihedral : 25.463 89.305 640 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 194.61 Ramachandran Plot: Outliers : 1.95 % Allowed : 57.42 % Favored : 40.62 % Rotamer: Outliers : 28.91 % Allowed : 31.25 % Favored : 39.84 % Cbeta Deviations : 47.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % 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: -9.14 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.96 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.179 0.025 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 164 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8055 (m-10) REVERT: A 7 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8902 (m-10) REVERT: I 102 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8845 (mmtm) REVERT: I 107 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.8535 (m-10) REVERT: J 206 LYS cc_start: 0.8879 (tttm) cc_final: 0.8389 (ttpp) REVERT: K 302 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8644 (tppp) REVERT: K 306 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8090 (mmmm) REVERT: L 103 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: M 202 LYS cc_start: 0.9243 (ttmm) cc_final: 0.8913 (ttmm) REVERT: M 206 LYS cc_start: 0.8785 (tttm) cc_final: 0.8409 (tttm) REVERT: N 302 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8809 (tppp) REVERT: N 304 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8034 (tm-30) REVERT: N 306 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8091 (mmmm) REVERT: N 307 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8190 (t80) REVERT: O 105 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8074 (m-10) REVERT: P 206 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8193 (ptmm) REVERT: Q 302 LYS cc_start: 0.8786 (tppp) cc_final: 0.8563 (tppp) REVERT: Q 303 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: Q 306 LYS cc_start: 0.8323 (mmmm) cc_final: 0.7970 (mmmm) REVERT: Q 307 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.7972 (t80) REVERT: S 202 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8152 (ttpp) REVERT: S 206 LYS cc_start: 0.8777 (tttm) cc_final: 0.7835 (ttpp) REVERT: T 304 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7448 (tm-30) REVERT: T 306 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8086 (mmtp) REVERT: E 6 LYS cc_start: 0.9158 (mmmm) cc_final: 0.8829 (ttmm) REVERT: U 103 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: U 106 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8418 (tppt) REVERT: V 202 LYS cc_start: 0.9373 (ttmm) cc_final: 0.8797 (ttmm) REVERT: V 206 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.7722 (ttpp) REVERT: W 302 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8387 (ttpp) REVERT: W 304 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7385 (tm-30) REVERT: W 306 LYS cc_start: 0.8664 (mmmm) cc_final: 0.7867 (mmtm) REVERT: F 5 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: X 103 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8724 (m-10) REVERT: X 106 LYS cc_start: 0.8917 (tppt) cc_final: 0.8320 (tppt) REVERT: Y 206 LYS cc_start: 0.8645 (tttm) cc_final: 0.8383 (tttm) REVERT: Z 302 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8194 (tppp) REVERT: Z 304 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8246 (tm-30) REVERT: Z 306 LYS cc_start: 0.8595 (mmmm) cc_final: 0.7999 (mmmm) REVERT: Z 307 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: G 5 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: i 102 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8708 (mmmt) REVERT: i 103 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8898 (m-80) REVERT: H 6 LYS cc_start: 0.9275 (mmmm) cc_final: 0.8982 (mmmm) REVERT: l 102 LYS cc_start: 0.9414 (mmtt) cc_final: 0.9182 (mmtm) REVERT: l 103 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: m 206 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8195 (pttm) REVERT: n 304 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7967 (tm-30) REVERT: n 306 LYS cc_start: 0.8760 (mmmm) cc_final: 0.8543 (mmmm) REVERT: a 2 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8507 (mtmm) REVERT: o 107 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8120 (t80) REVERT: p 203 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8205 (t80) REVERT: q 302 LYS cc_start: 0.9175 (tmtt) cc_final: 0.8744 (tmtt) REVERT: q 303 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7153 (t80) REVERT: q 305 PHE cc_start: 0.9040 (t80) cc_final: 0.8777 (t80) REVERT: q 306 LYS cc_start: 0.9014 (tttt) cc_final: 0.8548 (tttp) REVERT: q 307 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8025 (t80) REVERT: b 2 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8534 (mmtt) REVERT: r 102 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8265 (ttpp) REVERT: s 202 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8776 (tppp) REVERT: s 204 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8084 (tm-30) REVERT: t 303 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.7303 (t80) REVERT: c 2 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8581 (mmtt) REVERT: c 3 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7888 (t80) REVERT: u 102 LYS cc_start: 0.9002 (tptp) cc_final: 0.8763 (tptp) REVERT: v 204 GLU cc_start: 0.8617 (tm-30) cc_final: 0.7789 (tm-30) REVERT: v 207 PHE cc_start: 0.8804 (t80) cc_final: 0.7736 (t80) REVERT: x 104 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8615 (pp20) REVERT: y 203 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8291 (t80) REVERT: z 302 LYS cc_start: 0.8974 (tmtt) cc_final: 0.8463 (tmtt) REVERT: 1 203 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8294 (t80) REVERT: 2 306 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8360 (tmtt) REVERT: f 2 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8307 (mmtt) REVERT: 3 102 LYS cc_start: 0.9061 (tptp) cc_final: 0.8758 (tptp) REVERT: 4 202 LYS cc_start: 0.9119 (tptp) cc_final: 0.8692 (tppp) REVERT: 4 206 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8509 (tptp) REVERT: 5 306 LYS cc_start: 0.8879 (tttp) cc_final: 0.8345 (tttp) REVERT: 5 307 PHE cc_start: 0.8924 (t80) cc_final: 0.8657 (t80) REVERT: g 2 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8421 (mmtt) REVERT: 6 102 LYS cc_start: 0.9016 (tptp) cc_final: 0.8724 (ttpt) REVERT: 7 202 LYS cc_start: 0.9108 (tptp) cc_final: 0.8706 (tptp) REVERT: 7 203 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8216 (t80) REVERT: 8 307 PHE cc_start: 0.8526 (t80) cc_final: 0.8253 (t80) REVERT: 9 104 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7485 (tm-30) REVERT: AA 206 LYS cc_start: 0.8715 (tptp) cc_final: 0.8426 (tptp) REVERT: BA 302 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8809 (tmtt) REVERT: BA 307 PHE cc_start: 0.8871 (t80) cc_final: 0.8429 (t80) outliers start: 111 outliers final: 57 residues processed: 228 average time/residue: 0.3444 time to fit residues: 89.2302 Evaluate side-chains 261 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 163 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain K residue 305 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain Q residue 307 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 102 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 206 LYS Chi-restraints excluded: chain 5 residue 303 PHE Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 1.0006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.474 5568 Z= 8.460 Angle : 6.210 58.746 7232 Z= 2.752 Chirality : 0.417 1.081 512 Planarity : 0.027 0.091 960 Dihedral : 25.385 89.204 640 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 196.32 Ramachandran Plot: Outliers : 1.56 % Allowed : 57.03 % Favored : 41.41 % Rotamer: Outliers : 27.86 % Allowed : 32.55 % Favored : 39.58 % Cbeta Deviations : 46.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.35 % 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: -9.14 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.97 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE 5 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 164 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8066 (m-10) REVERT: A 7 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8902 (m-10) REVERT: I 102 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8852 (mmtm) REVERT: I 107 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8536 (m-10) REVERT: J 206 LYS cc_start: 0.8911 (tttm) cc_final: 0.8491 (ttpp) REVERT: K 302 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8682 (tppp) REVERT: K 306 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8089 (mmmm) REVERT: L 103 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8645 (m-80) REVERT: M 202 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8918 (ttmm) REVERT: M 206 LYS cc_start: 0.8782 (tttm) cc_final: 0.8406 (tttm) REVERT: N 302 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8749 (tppp) REVERT: N 304 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8027 (tm-30) REVERT: N 306 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8113 (mmmm) REVERT: N 307 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8191 (t80) REVERT: O 105 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: P 206 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8255 (ptmm) REVERT: Q 303 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: S 202 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8134 (ttpp) REVERT: S 206 LYS cc_start: 0.8692 (tttm) cc_final: 0.7785 (ttpp) REVERT: T 304 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7435 (tm-30) REVERT: T 306 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8093 (mmtp) REVERT: E 6 LYS cc_start: 0.9160 (mmmm) cc_final: 0.8835 (ttmm) REVERT: U 103 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: U 106 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8432 (tppt) REVERT: V 202 LYS cc_start: 0.9416 (ttmm) cc_final: 0.9044 (ttmm) REVERT: W 302 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8471 (ttpp) REVERT: W 304 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7470 (tm-30) REVERT: F 5 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: X 103 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8715 (m-10) REVERT: X 106 LYS cc_start: 0.8921 (tppt) cc_final: 0.8308 (tppt) REVERT: Y 206 LYS cc_start: 0.8641 (tttm) cc_final: 0.8395 (tttm) REVERT: Z 302 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8169 (tppp) REVERT: Z 304 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8312 (tm-30) REVERT: Z 306 LYS cc_start: 0.8592 (mmmm) cc_final: 0.7985 (mmmm) REVERT: Z 307 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: G 5 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: i 102 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8682 (mmmt) REVERT: i 103 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8914 (m-80) REVERT: H 6 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8991 (mmmm) REVERT: l 102 LYS cc_start: 0.9413 (mmtm) cc_final: 0.9162 (mmtm) REVERT: l 103 PHE cc_start: 0.8829 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: m 206 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8191 (pttm) REVERT: n 302 LYS cc_start: 0.8873 (tppp) cc_final: 0.8662 (tppp) REVERT: n 304 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7972 (tm-30) REVERT: a 2 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8515 (mtmm) REVERT: o 107 PHE cc_start: 0.8984 (OUTLIER) cc_final: 0.8112 (t80) REVERT: p 203 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8206 (t80) REVERT: q 302 LYS cc_start: 0.9178 (tmtt) cc_final: 0.8759 (tmtt) REVERT: q 303 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.7141 (t80) REVERT: q 305 PHE cc_start: 0.9039 (t80) cc_final: 0.8760 (t80) REVERT: q 306 LYS cc_start: 0.9013 (tttt) cc_final: 0.8561 (tttp) REVERT: q 307 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8028 (t80) REVERT: b 2 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8532 (mmtt) REVERT: r 102 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8179 (ttpp) REVERT: s 202 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8781 (tppp) REVERT: s 204 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8081 (tm-30) REVERT: t 303 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7369 (t80) REVERT: c 2 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8593 (mmtt) REVERT: c 3 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7891 (t80) REVERT: u 102 LYS cc_start: 0.9074 (tptp) cc_final: 0.8827 (tptp) REVERT: v 204 GLU cc_start: 0.8611 (tm-30) cc_final: 0.7773 (tm-30) REVERT: v 207 PHE cc_start: 0.8796 (t80) cc_final: 0.7733 (t80) REVERT: x 104 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8644 (pp20) REVERT: y 203 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8328 (t80) REVERT: z 302 LYS cc_start: 0.8976 (tmtt) cc_final: 0.8461 (tmtt) REVERT: 1 203 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8324 (t80) REVERT: 2 306 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8359 (tmtt) REVERT: f 2 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8268 (mmtt) REVERT: 3 102 LYS cc_start: 0.9074 (tptp) cc_final: 0.8775 (tptp) REVERT: 4 202 LYS cc_start: 0.9118 (tptp) cc_final: 0.8685 (tppp) REVERT: 4 206 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8494 (tptp) REVERT: 5 306 LYS cc_start: 0.8898 (tttp) cc_final: 0.8359 (tttp) REVERT: 5 307 PHE cc_start: 0.8922 (t80) cc_final: 0.8671 (t80) REVERT: 6 102 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8728 (ttpt) REVERT: 7 203 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8401 (t80) REVERT: 8 307 PHE cc_start: 0.8502 (t80) cc_final: 0.8226 (t80) REVERT: 9 104 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7484 (tm-30) REVERT: AA 206 LYS cc_start: 0.8719 (tptp) cc_final: 0.8447 (tptp) REVERT: BA 307 PHE cc_start: 0.8840 (t80) cc_final: 0.8412 (t80) outliers start: 107 outliers final: 56 residues processed: 226 average time/residue: 0.3478 time to fit residues: 89.2325 Evaluate side-chains 258 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 162 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain K residue 305 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain x residue 104 GLU Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 206 LYS Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 102 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 1.0043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.473 5568 Z= 8.452 Angle : 6.222 58.705 7232 Z= 2.755 Chirality : 0.416 1.083 512 Planarity : 0.027 0.091 960 Dihedral : 25.395 89.218 640 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 197.85 Ramachandran Plot: Outliers : 1.95 % Allowed : 56.64 % Favored : 41.41 % Rotamer: Outliers : 28.39 % Allowed : 33.85 % Favored : 37.76 % Cbeta Deviations : 47.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % 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: -9.11 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.94 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE P 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 165 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.8064 (m-10) REVERT: A 7 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8910 (m-10) REVERT: I 102 LYS cc_start: 0.9032 (mmtm) cc_final: 0.8816 (mmtm) REVERT: I 107 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8543 (m-10) REVERT: J 206 LYS cc_start: 0.8892 (tttm) cc_final: 0.8525 (ttpp) REVERT: K 302 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8687 (tppp) REVERT: K 306 LYS cc_start: 0.8688 (mmmm) cc_final: 0.8104 (mmmm) REVERT: B 6 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8722 (mmmm) REVERT: L 103 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: M 202 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8913 (ttmm) REVERT: M 206 LYS cc_start: 0.8796 (tttm) cc_final: 0.8410 (tttm) REVERT: N 302 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8749 (tppp) REVERT: N 304 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8033 (tm-30) REVERT: N 306 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8118 (mmmm) REVERT: N 307 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8181 (t80) REVERT: O 105 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: P 206 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8247 (ptmm) REVERT: Q 303 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: S 202 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8132 (ttpp) REVERT: S 206 LYS cc_start: 0.8631 (tttm) cc_final: 0.7890 (ttpp) REVERT: T 304 GLU cc_start: 0.8393 (tm-30) cc_final: 0.7449 (tm-30) REVERT: T 306 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8088 (mmtp) REVERT: E 6 LYS cc_start: 0.9164 (mmmm) cc_final: 0.8840 (ttmm) REVERT: U 103 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: U 106 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8448 (tppt) REVERT: V 202 LYS cc_start: 0.9406 (ttmm) cc_final: 0.8934 (ttmm) REVERT: V 206 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8119 (ttpp) REVERT: W 302 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8426 (ttpp) REVERT: W 304 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7118 (tm-30) REVERT: W 307 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8094 (t80) REVERT: F 5 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: X 103 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8637 (m-10) REVERT: X 106 LYS cc_start: 0.8907 (tppt) cc_final: 0.8326 (tppt) REVERT: Y 206 LYS cc_start: 0.8645 (tttm) cc_final: 0.8408 (tttm) REVERT: Z 302 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8185 (tppp) REVERT: Z 304 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8309 (tm-30) REVERT: Z 306 LYS cc_start: 0.8573 (mmmm) cc_final: 0.7970 (mmmm) REVERT: Z 307 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: G 5 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: G 6 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8488 (ttmm) REVERT: i 102 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8674 (mmmt) REVERT: i 103 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8907 (m-80) REVERT: j 202 LYS cc_start: 0.9256 (ttmm) cc_final: 0.8892 (ttmm) REVERT: k 303 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.7033 (m-10) REVERT: H 6 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8991 (mmmm) REVERT: l 102 LYS cc_start: 0.9407 (mmtm) cc_final: 0.9160 (mmtm) REVERT: l 103 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: m 206 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8200 (pttm) REVERT: n 302 LYS cc_start: 0.8957 (tppp) cc_final: 0.8686 (tppp) REVERT: n 304 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7975 (tm-30) REVERT: a 2 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8522 (mtmm) REVERT: o 107 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8104 (t80) REVERT: p 203 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8209 (t80) REVERT: q 302 LYS cc_start: 0.9169 (tmtt) cc_final: 0.8733 (tmtt) REVERT: q 303 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.7139 (t80) REVERT: q 305 PHE cc_start: 0.9037 (t80) cc_final: 0.8755 (t80) REVERT: q 306 LYS cc_start: 0.9013 (tttt) cc_final: 0.8550 (tttp) REVERT: q 307 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8023 (t80) REVERT: b 2 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8534 (mmtt) REVERT: r 102 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8148 (ttpp) REVERT: s 202 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8790 (tppp) REVERT: s 204 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8054 (tm-30) REVERT: t 303 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7377 (t80) REVERT: c 2 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8581 (mmtt) REVERT: c 3 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7906 (t80) REVERT: v 204 GLU cc_start: 0.8603 (tm-30) cc_final: 0.7761 (tm-30) REVERT: v 207 PHE cc_start: 0.8789 (t80) cc_final: 0.7724 (t80) REVERT: y 203 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8328 (t80) REVERT: z 302 LYS cc_start: 0.8971 (tmtt) cc_final: 0.8458 (tmtt) REVERT: 1 203 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8338 (t80) REVERT: 2 306 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8362 (tmtt) REVERT: f 2 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8252 (mmtt) REVERT: 3 102 LYS cc_start: 0.9069 (tptp) cc_final: 0.8783 (tptp) REVERT: 4 202 LYS cc_start: 0.9110 (tptp) cc_final: 0.8678 (tppp) REVERT: 4 206 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8489 (tptp) REVERT: 5 306 LYS cc_start: 0.8841 (tttp) cc_final: 0.8323 (tttp) REVERT: 5 307 PHE cc_start: 0.8920 (t80) cc_final: 0.8671 (t80) REVERT: g 2 LYS cc_start: 0.8841 (mmtt) cc_final: 0.8416 (mtmm) REVERT: 6 102 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8724 (tptp) REVERT: 7 203 PHE cc_start: 0.8714 (OUTLIER) cc_final: 0.8469 (t80) REVERT: 9 104 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7499 (tm-30) REVERT: AA 206 LYS cc_start: 0.8714 (tptp) cc_final: 0.8434 (tptp) REVERT: BA 307 PHE cc_start: 0.8836 (t80) cc_final: 0.8416 (t80) outliers start: 109 outliers final: 56 residues processed: 227 average time/residue: 0.3588 time to fit residues: 92.4079 Evaluate side-chains 262 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 164 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain K residue 305 PHE Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain W residue 307 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 303 PHE Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 206 LYS Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 102 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 1.0077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.475 5568 Z= 8.455 Angle : 6.234 58.767 7232 Z= 2.757 Chirality : 0.417 1.084 512 Planarity : 0.027 0.088 960 Dihedral : 25.414 88.950 640 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 197.98 Ramachandran Plot: Outliers : 1.95 % Allowed : 57.42 % Favored : 40.62 % Rotamer: Outliers : 27.08 % Allowed : 35.94 % Favored : 36.98 % Cbeta Deviations : 46.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % 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: -9.11 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.94 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE P 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 167 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.8062 (m-10) REVERT: A 7 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8914 (m-10) REVERT: I 102 LYS cc_start: 0.9050 (mmtm) cc_final: 0.8841 (mmtm) REVERT: I 107 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8541 (m-10) REVERT: J 206 LYS cc_start: 0.8879 (tttm) cc_final: 0.8544 (ttpp) REVERT: K 302 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8679 (tppp) REVERT: K 306 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8099 (mmmm) REVERT: B 6 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8726 (mmmm) REVERT: L 103 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: M 202 LYS cc_start: 0.9251 (ttmm) cc_final: 0.8917 (ttmm) REVERT: M 206 LYS cc_start: 0.8792 (tttm) cc_final: 0.8399 (tttm) REVERT: N 302 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8760 (tppp) REVERT: N 304 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8033 (tm-30) REVERT: N 306 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8117 (mmmm) REVERT: N 307 PHE cc_start: 0.8837 (OUTLIER) cc_final: 0.8175 (t80) REVERT: O 105 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.8067 (m-10) REVERT: P 206 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8266 (ptmm) REVERT: Q 303 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: S 202 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8135 (ttpp) REVERT: S 206 LYS cc_start: 0.8606 (tttm) cc_final: 0.7897 (ttpp) REVERT: T 304 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7446 (tm-30) REVERT: T 306 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8085 (mmtp) REVERT: E 6 LYS cc_start: 0.9182 (mmmm) cc_final: 0.8878 (ttmm) REVERT: U 103 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: U 106 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8439 (tppt) REVERT: V 202 LYS cc_start: 0.9424 (ttmm) cc_final: 0.8952 (ttmm) REVERT: W 302 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8427 (ttpp) REVERT: W 307 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8086 (t80) REVERT: F 5 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: X 103 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8630 (m-10) REVERT: X 106 LYS cc_start: 0.8955 (tppt) cc_final: 0.8362 (tppt) REVERT: Y 206 LYS cc_start: 0.8645 (tttm) cc_final: 0.8403 (tttm) REVERT: Z 302 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8183 (tppp) REVERT: Z 304 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8277 (tm-30) REVERT: Z 306 LYS cc_start: 0.8585 (mmmm) cc_final: 0.7982 (mmmm) REVERT: Z 307 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: G 5 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: G 6 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8422 (ttmm) REVERT: i 102 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8678 (mmmt) REVERT: i 103 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8888 (m-80) REVERT: H 6 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8993 (mmmm) REVERT: l 102 LYS cc_start: 0.9406 (mmtm) cc_final: 0.9160 (mmtm) REVERT: l 103 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: m 206 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8238 (pttm) REVERT: n 302 LYS cc_start: 0.8957 (tppp) cc_final: 0.8736 (tppp) REVERT: n 304 GLU cc_start: 0.8525 (tm-30) cc_final: 0.7993 (tm-30) REVERT: a 2 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8523 (mtmm) REVERT: o 107 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8096 (t80) REVERT: p 203 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8212 (t80) REVERT: q 302 LYS cc_start: 0.9168 (tmtt) cc_final: 0.8736 (tmtt) REVERT: q 303 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.7132 (t80) REVERT: q 305 PHE cc_start: 0.9040 (t80) cc_final: 0.8760 (t80) REVERT: q 306 LYS cc_start: 0.9012 (tttt) cc_final: 0.8557 (tttp) REVERT: q 307 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8031 (t80) REVERT: b 2 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8483 (mmtt) REVERT: r 102 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8147 (ttpp) REVERT: s 202 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8793 (tppp) REVERT: s 204 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8060 (tm-30) REVERT: t 303 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7383 (t80) REVERT: c 2 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8547 (mmtt) REVERT: c 3 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7914 (t80) REVERT: v 204 GLU cc_start: 0.8608 (tm-30) cc_final: 0.7760 (tm-30) REVERT: v 207 PHE cc_start: 0.8766 (t80) cc_final: 0.7701 (t80) REVERT: x 104 GLU cc_start: 0.8825 (pp20) cc_final: 0.8488 (pp20) REVERT: y 203 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8328 (t80) REVERT: z 302 LYS cc_start: 0.8970 (tmtt) cc_final: 0.8457 (tmtt) REVERT: 1 203 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8340 (t80) REVERT: 2 306 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8349 (tmtt) REVERT: f 2 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8237 (mmtt) REVERT: f 5 PHE cc_start: 0.8568 (t80) cc_final: 0.8355 (t80) REVERT: 3 102 LYS cc_start: 0.9055 (tptp) cc_final: 0.8779 (tptp) REVERT: 4 202 LYS cc_start: 0.9105 (tptp) cc_final: 0.8679 (tppp) REVERT: 4 206 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8506 (tptp) REVERT: 5 306 LYS cc_start: 0.8855 (tttp) cc_final: 0.8346 (tttp) REVERT: 5 307 PHE cc_start: 0.8921 (t80) cc_final: 0.8668 (t80) REVERT: g 2 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8417 (mtmm) REVERT: 6 102 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8729 (tptp) REVERT: 7 202 LYS cc_start: 0.9127 (tptp) cc_final: 0.8735 (tptp) REVERT: 7 203 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8209 (t80) REVERT: 9 102 LYS cc_start: 0.9012 (tptp) cc_final: 0.8637 (tptp) REVERT: 9 104 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7774 (tm-30) REVERT: AA 206 LYS cc_start: 0.8727 (tptp) cc_final: 0.8465 (tptp) REVERT: BA 307 PHE cc_start: 0.8846 (t80) cc_final: 0.8475 (t80) outliers start: 104 outliers final: 56 residues processed: 226 average time/residue: 0.3731 time to fit residues: 95.5692 Evaluate side-chains 261 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 164 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 305 PHE Chi-restraints excluded: chain W residue 307 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain r residue 102 LYS Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 206 LYS Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 102 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 1.0096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.475 5568 Z= 8.460 Angle : 6.234 58.791 7232 Z= 2.756 Chirality : 0.417 1.083 512 Planarity : 0.027 0.088 960 Dihedral : 25.405 89.807 640 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 200.16 Ramachandran Plot: Outliers : 1.95 % Allowed : 56.25 % Favored : 41.80 % Rotamer: Outliers : 27.34 % Allowed : 36.46 % Favored : 36.20 % Cbeta Deviations : 46.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % 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: -9.15 (0.23), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.97 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.178 0.025 PHE P 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 166 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.8065 (m-10) REVERT: A 7 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8916 (m-10) REVERT: I 102 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8831 (mmtm) REVERT: I 107 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8536 (m-10) REVERT: J 206 LYS cc_start: 0.8882 (tttm) cc_final: 0.8555 (ttpp) REVERT: K 302 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8677 (tppp) REVERT: K 306 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8120 (mmmm) REVERT: B 6 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8727 (mmmm) REVERT: L 103 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: M 202 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8918 (ttmm) REVERT: M 206 LYS cc_start: 0.8791 (tttm) cc_final: 0.8399 (tttm) REVERT: N 302 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8766 (tppp) REVERT: N 304 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8034 (tm-30) REVERT: N 306 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8123 (mmmm) REVERT: N 307 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8183 (t80) REVERT: O 105 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.8067 (m-10) REVERT: P 206 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8255 (ptmm) REVERT: Q 303 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: S 202 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.8126 (ttpp) REVERT: S 206 LYS cc_start: 0.8609 (tttm) cc_final: 0.7746 (ttpp) REVERT: T 304 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7455 (tm-30) REVERT: T 306 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8083 (mmtp) REVERT: E 6 LYS cc_start: 0.9183 (mmmm) cc_final: 0.8879 (ttmm) REVERT: U 103 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: U 106 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8437 (tppt) REVERT: W 307 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8105 (t80) REVERT: F 5 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: X 103 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8634 (m-10) REVERT: X 106 LYS cc_start: 0.8940 (tppt) cc_final: 0.8356 (tppt) REVERT: Y 202 LYS cc_start: 0.9206 (ttmm) cc_final: 0.8892 (ttmm) REVERT: Y 206 LYS cc_start: 0.8649 (tttm) cc_final: 0.8409 (tttm) REVERT: Z 302 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8077 (tppp) REVERT: Z 304 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8296 (tm-30) REVERT: Z 306 LYS cc_start: 0.8583 (mmmm) cc_final: 0.7938 (mmmm) REVERT: Z 307 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: G 5 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: G 6 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8428 (ttmm) REVERT: i 102 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8676 (mmmt) REVERT: i 103 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8928 (m-80) REVERT: k 303 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6911 (m-10) REVERT: H 6 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8994 (mmmm) REVERT: l 102 LYS cc_start: 0.9407 (mmtm) cc_final: 0.9163 (mmtm) REVERT: l 103 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: m 206 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8237 (pttm) REVERT: n 302 LYS cc_start: 0.8950 (tppp) cc_final: 0.8741 (tppp) REVERT: n 304 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7999 (tm-30) REVERT: a 2 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8524 (mtmm) REVERT: o 107 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8099 (t80) REVERT: p 203 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8255 (t80) REVERT: q 302 LYS cc_start: 0.9168 (tmtt) cc_final: 0.8737 (tmtt) REVERT: q 303 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7150 (t80) REVERT: q 305 PHE cc_start: 0.9040 (t80) cc_final: 0.8764 (t80) REVERT: q 306 LYS cc_start: 0.9011 (tttt) cc_final: 0.8556 (tttp) REVERT: q 307 PHE cc_start: 0.8728 (OUTLIER) cc_final: 0.8031 (t80) REVERT: b 2 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8486 (mmtt) REVERT: s 202 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8796 (tppp) REVERT: s 204 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8058 (tm-30) REVERT: t 303 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.7379 (t80) REVERT: c 2 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8545 (mmtt) REVERT: c 3 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7918 (t80) REVERT: v 204 GLU cc_start: 0.8604 (tm-30) cc_final: 0.7755 (tm-30) REVERT: v 207 PHE cc_start: 0.8764 (t80) cc_final: 0.7704 (t80) REVERT: x 104 GLU cc_start: 0.8826 (pp20) cc_final: 0.8467 (pp20) REVERT: y 203 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8328 (t80) REVERT: z 302 LYS cc_start: 0.8968 (tmtt) cc_final: 0.8458 (tmtt) REVERT: 1 203 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8371 (t80) REVERT: 2 306 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8371 (tmtt) REVERT: f 2 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8242 (mmtt) REVERT: 3 102 LYS cc_start: 0.9058 (tptp) cc_final: 0.8787 (tptp) REVERT: 4 202 LYS cc_start: 0.9104 (tptp) cc_final: 0.8676 (tppp) REVERT: 4 206 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8485 (tptp) REVERT: 5 306 LYS cc_start: 0.8858 (tttp) cc_final: 0.8348 (tttp) REVERT: 5 307 PHE cc_start: 0.8920 (t80) cc_final: 0.8668 (t80) REVERT: g 2 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8418 (mtmm) REVERT: 6 102 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8730 (tptp) REVERT: 7 202 LYS cc_start: 0.9125 (tptp) cc_final: 0.8734 (tptp) REVERT: 7 203 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8174 (t80) REVERT: 9 102 LYS cc_start: 0.9001 (tptp) cc_final: 0.8623 (tptp) REVERT: 9 104 GLU cc_start: 0.8497 (tm-30) cc_final: 0.7730 (tm-30) REVERT: AA 206 LYS cc_start: 0.8716 (tptp) cc_final: 0.8459 (tptp) REVERT: BA 307 PHE cc_start: 0.8850 (t80) cc_final: 0.8507 (t80) outliers start: 105 outliers final: 60 residues processed: 227 average time/residue: 0.3451 time to fit residues: 88.6045 Evaluate side-chains 265 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 165 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 PHE Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain I residue 103 PHE Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 107 PHE Chi-restraints excluded: chain J residue 202 LYS Chi-restraints excluded: chain J residue 207 PHE Chi-restraints excluded: chain K residue 302 LYS Chi-restraints excluded: chain B residue 4 GLU Chi-restraints excluded: chain B residue 6 LYS Chi-restraints excluded: chain L residue 103 PHE Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain N residue 302 LYS Chi-restraints excluded: chain N residue 307 PHE Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain O residue 103 PHE Chi-restraints excluded: chain O residue 105 PHE Chi-restraints excluded: chain P residue 206 LYS Chi-restraints excluded: chain P residue 207 PHE Chi-restraints excluded: chain Q residue 303 PHE Chi-restraints excluded: chain Q residue 305 PHE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain S residue 202 LYS Chi-restraints excluded: chain T residue 302 LYS Chi-restraints excluded: chain T residue 306 LYS Chi-restraints excluded: chain U residue 102 LYS Chi-restraints excluded: chain U residue 103 PHE Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain V residue 204 GLU Chi-restraints excluded: chain V residue 206 LYS Chi-restraints excluded: chain W residue 302 LYS Chi-restraints excluded: chain W residue 307 PHE Chi-restraints excluded: chain F residue 5 PHE Chi-restraints excluded: chain X residue 102 LYS Chi-restraints excluded: chain X residue 103 PHE Chi-restraints excluded: chain Y residue 204 GLU Chi-restraints excluded: chain Z residue 302 LYS Chi-restraints excluded: chain Z residue 305 PHE Chi-restraints excluded: chain Z residue 307 PHE Chi-restraints excluded: chain G residue 5 PHE Chi-restraints excluded: chain i residue 103 PHE Chi-restraints excluded: chain i residue 106 LYS Chi-restraints excluded: chain j residue 203 PHE Chi-restraints excluded: chain j residue 204 GLU Chi-restraints excluded: chain k residue 302 LYS Chi-restraints excluded: chain k residue 303 PHE Chi-restraints excluded: chain k residue 305 PHE Chi-restraints excluded: chain k residue 306 LYS Chi-restraints excluded: chain H residue 7 PHE Chi-restraints excluded: chain l residue 103 PHE Chi-restraints excluded: chain m residue 204 GLU Chi-restraints excluded: chain m residue 206 LYS Chi-restraints excluded: chain o residue 104 GLU Chi-restraints excluded: chain o residue 107 PHE Chi-restraints excluded: chain p residue 203 PHE Chi-restraints excluded: chain q residue 303 PHE Chi-restraints excluded: chain q residue 307 PHE Chi-restraints excluded: chain b residue 2 LYS Chi-restraints excluded: chain b residue 5 PHE Chi-restraints excluded: chain r residue 104 GLU Chi-restraints excluded: chain s residue 202 LYS Chi-restraints excluded: chain t residue 303 PHE Chi-restraints excluded: chain t residue 304 GLU Chi-restraints excluded: chain t residue 306 LYS Chi-restraints excluded: chain c residue 2 LYS Chi-restraints excluded: chain c residue 3 PHE Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain u residue 105 PHE Chi-restraints excluded: chain u residue 106 LYS Chi-restraints excluded: chain u residue 107 PHE Chi-restraints excluded: chain v residue 206 LYS Chi-restraints excluded: chain w residue 303 PHE Chi-restraints excluded: chain w residue 305 PHE Chi-restraints excluded: chain w residue 306 LYS Chi-restraints excluded: chain x residue 103 PHE Chi-restraints excluded: chain y residue 203 PHE Chi-restraints excluded: chain e residue 5 PHE Chi-restraints excluded: chain 0 residue 103 PHE Chi-restraints excluded: chain 1 residue 203 PHE Chi-restraints excluded: chain 2 residue 303 PHE Chi-restraints excluded: chain 2 residue 306 LYS Chi-restraints excluded: chain 3 residue 104 GLU Chi-restraints excluded: chain 3 residue 106 LYS Chi-restraints excluded: chain 4 residue 203 PHE Chi-restraints excluded: chain 4 residue 206 LYS Chi-restraints excluded: chain 5 residue 305 PHE Chi-restraints excluded: chain 6 residue 102 LYS Chi-restraints excluded: chain 6 residue 103 PHE Chi-restraints excluded: chain 6 residue 104 GLU Chi-restraints excluded: chain 7 residue 203 PHE Chi-restraints excluded: chain 7 residue 205 PHE Chi-restraints excluded: chain 8 residue 305 PHE Chi-restraints excluded: chain h residue 2 LYS Chi-restraints excluded: chain 9 residue 106 LYS Chi-restraints excluded: chain AA residue 202 LYS Chi-restraints excluded: chain BA residue 303 PHE Chi-restraints excluded: chain BA residue 306 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.053633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.046587 restraints weight = 20421.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.048334 restraints weight = 11012.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.049521 restraints weight = 6894.995| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 1.0115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.154 0.477 5568 Z= 8.462 Angle : 6.234 58.758 7232 Z= 2.756 Chirality : 0.417 1.082 512 Planarity : 0.027 0.088 960 Dihedral : 25.386 89.424 640 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 199.55 Ramachandran Plot: Outliers : 1.56 % Allowed : 58.20 % Favored : 40.23 % Rotamer: Outliers : 28.12 % Allowed : 35.94 % Favored : 35.94 % Cbeta Deviations : 46.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.57 % 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: -9.11 (0.24), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.94 (0.18), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.177 0.025 PHE P 205 =============================================================================== Job complete usr+sys time: 1382.07 seconds wall clock time: 25 minutes 54.48 seconds (1554.48 seconds total)