Starting phenix.real_space_refine on Sun Sep 29 10:46:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/09_2024/6z9f_11122.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/09_2024/6z9f_11122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/09_2024/6z9f_11122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/09_2024/6z9f_11122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/09_2024/6z9f_11122.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z9f_11122/09_2024/6z9f_11122.cif" } resolution = 1.56 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= -0.156 sd= 10.228 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 41020 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 120 5.16 5 Na 32 4.78 5 C 23040 2.51 5 N 6528 2.21 5 O 11300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 432 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 41020 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "1" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "K" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "a" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "B" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "E" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "e" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "r" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "G" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "I" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "M" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "O" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "Q" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "S" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "U" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "W" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "Y" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "2" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "4" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "F" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "H" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "P" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "X" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "6" Number of atoms: 1534 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1418 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1319 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Classifications: {'water': 172} Link IDs: {None: 171} Chain: "1" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "K" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "a" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Classifications: {'water': 172} Link IDs: {None: 171} Chain: "B" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "E" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "e" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "r" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "G" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "I" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "M" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "O" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 177 Classifications: {'water': 177} Link IDs: {None: 176} Chain: "Q" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "S" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "U" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Chain: "W" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "Y" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "2" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "4" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "F" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "H" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "P" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "X" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 171 Classifications: {'water': 171} Link IDs: {None: 170} Chain: "6" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Classifications: {'water': 175} Link IDs: {None: 174} Residues with excluded nonbonded symmetry interactions: 312 residue: pdb=" N ALYS A 49 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 49 " occ=0.50 residue: pdb=" N ALYS A 53 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 53 " occ=0.50 residue: pdb=" N AGLU A 64 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 64 " occ=0.50 residue: pdb=" N ALYS A 68 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 68 " occ=0.50 residue: pdb=" N ALYS A 71 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 71 " occ=0.50 residue: pdb=" N ALEU A 72 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 72 " occ=0.50 residue: pdb=" N AGLN A 75 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 75 " occ=0.50 residue: pdb=" N AGLU A 94 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 94 " occ=0.50 residue: pdb=" N AASN A 109 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 109 " occ=0.50 residue: pdb=" N AILE A 133 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.50 residue: pdb=" N AARG A 156 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 156 " occ=0.50 residue: pdb=" N AGLU A 162 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 162 " occ=0.50 ... (remaining 300 not shown) Time building chain proxies: 28.80, per 1000 atoms: 0.70 Number of scatterers: 41020 At special positions: 0 Unit cell: (136.284, 136.284, 136.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 Na 32 11.00 O 11300 8.00 N 6528 7.00 C 23040 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: 8.54 Conformation dependent library (CDL) restraints added in 6.0 seconds 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8592 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.771A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 42 Processing helix chain '1' and resid 48 through 77 Processing helix chain '1' and resid 95 through 124 Processing helix chain '1' and resid 126 through 137 Processing helix chain '1' and resid 137 through 159 Processing helix chain '1' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU 1 167 " --> pdb=" O SER 1 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 77 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU K 167 " --> pdb=" O SER K 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 42 Processing helix chain 'a' and resid 48 through 77 Processing helix chain 'a' and resid 95 through 124 Processing helix chain 'a' and resid 126 through 137 Processing helix chain 'a' and resid 137 through 159 Processing helix chain 'a' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU a 167 " --> pdb=" O SER a 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 77 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) Processing helix chain 'e' and resid 13 through 42 Processing helix chain 'e' and resid 48 through 77 Processing helix chain 'e' and resid 95 through 124 Processing helix chain 'e' and resid 126 through 137 Processing helix chain 'e' and resid 137 through 159 Processing helix chain 'e' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU e 167 " --> pdb=" O SER e 163 " (cutoff:3.500A) Processing helix chain 'r' and resid 13 through 42 Processing helix chain 'r' and resid 48 through 77 Processing helix chain 'r' and resid 95 through 124 Processing helix chain 'r' and resid 126 through 137 Processing helix chain 'r' and resid 137 through 159 Processing helix chain 'r' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU r 167 " --> pdb=" O SER r 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 77 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 3.771A pdb=" N GLU G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 3.771A pdb=" N GLU I 167 " --> pdb=" O SER I 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 77 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 3.771A pdb=" N GLU M 167 " --> pdb=" O SER M 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 77 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 3.771A pdb=" N GLU O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 77 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 77 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU S 167 " --> pdb=" O SER S 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 77 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU U 167 " --> pdb=" O SER U 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 77 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU W 167 " --> pdb=" O SER W 163 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 42 Processing helix chain 'Y' and resid 48 through 77 Processing helix chain 'Y' and resid 95 through 124 Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 137 through 159 Processing helix chain 'Y' and resid 163 through 174 removed outlier: 3.771A pdb=" N GLU Y 167 " --> pdb=" O SER Y 163 " (cutoff:3.500A) Processing helix chain '2' and resid 13 through 42 Processing helix chain '2' and resid 48 through 77 Processing helix chain '2' and resid 95 through 124 Processing helix chain '2' and resid 126 through 137 Processing helix chain '2' and resid 137 through 159 Processing helix chain '2' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU 2 167 " --> pdb=" O SER 2 163 " (cutoff:3.500A) Processing helix chain '4' and resid 13 through 42 Processing helix chain '4' and resid 48 through 77 Processing helix chain '4' and resid 95 through 124 Processing helix chain '4' and resid 126 through 137 Processing helix chain '4' and resid 137 through 159 Processing helix chain '4' and resid 163 through 174 removed outlier: 3.771A pdb=" N GLU 4 167 " --> pdb=" O SER 4 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 77 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 77 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU P 167 " --> pdb=" O SER P 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 77 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU X 167 " --> pdb=" O SER X 163 " (cutoff:3.500A) Processing helix chain '6' and resid 13 through 42 Processing helix chain '6' and resid 48 through 77 Processing helix chain '6' and resid 95 through 124 Processing helix chain '6' and resid 126 through 137 Processing helix chain '6' and resid 137 through 159 Processing helix chain '6' and resid 163 through 174 removed outlier: 3.772A pdb=" N GLU 6 167 " --> pdb=" O SER 6 163 " (cutoff:3.500A) 3024 hydrogen bonds defined for protein. 9312 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: 11.10 Time building geometry restraints manager: 9.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6750 1.31 - 1.44: 9924 1.44 - 1.57: 20910 1.57 - 1.70: 0 1.70 - 1.83: 216 Bond restraints: 37800 Sorted by residual: bond pdb=" CE1 HIS I 13 " pdb=" NE2 HIS I 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.17e+01 bond pdb=" CE1 HIS X 13 " pdb=" NE2 HIS X 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.17e+01 bond pdb=" CE1 HIS 1 13 " pdb=" NE2 HIS 1 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 bond pdb=" CE1 HIS P 13 " pdb=" NE2 HIS P 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 bond pdb=" CE1 HIS S 13 " pdb=" NE2 HIS S 13 " ideal model delta sigma weight residual 1.321 1.377 -0.056 1.00e-02 1.00e+04 3.11e+01 ... (remaining 37795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 35363 1.71 - 3.42: 13458 3.42 - 5.12: 2059 5.12 - 6.83: 357 6.83 - 8.54: 27 Bond angle restraints: 51264 Sorted by residual: angle pdb=" CA LEU P 138 " pdb=" C LEU P 138 " pdb=" O LEU P 138 " ideal model delta sigma weight residual 120.82 115.30 5.52 1.05e+00 9.07e-01 2.76e+01 angle pdb=" CA LEU e 138 " pdb=" C LEU e 138 " pdb=" O LEU e 138 " ideal model delta sigma weight residual 120.82 115.30 5.52 1.05e+00 9.07e-01 2.76e+01 angle pdb=" CA LEU 1 138 " pdb=" C LEU 1 138 " pdb=" O LEU 1 138 " ideal model delta sigma weight residual 120.82 115.31 5.51 1.05e+00 9.07e-01 2.76e+01 angle pdb=" CA LEU M 138 " pdb=" C LEU M 138 " pdb=" O LEU M 138 " ideal model delta sigma weight residual 120.82 115.32 5.50 1.05e+00 9.07e-01 2.74e+01 angle pdb=" CA LEU B 138 " pdb=" C LEU B 138 " pdb=" O LEU B 138 " ideal model delta sigma weight residual 120.82 115.32 5.50 1.05e+00 9.07e-01 2.74e+01 ... (remaining 51259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 21023 16.14 - 32.28: 1295 32.28 - 48.42: 490 48.42 - 64.55: 328 64.55 - 80.69: 72 Dihedral angle restraints: 23208 sinusoidal: 9672 harmonic: 13536 Sorted by residual: dihedral pdb=" C TYR H 39 " pdb=" N TYR H 39 " pdb=" CA TYR H 39 " pdb=" CB TYR H 39 " ideal model delta harmonic sigma weight residual -122.60 -132.85 10.25 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C TYR A 39 " pdb=" N TYR A 39 " pdb=" CA TYR A 39 " pdb=" CB TYR A 39 " ideal model delta harmonic sigma weight residual -122.60 -132.84 10.24 0 2.50e+00 1.60e-01 1.68e+01 dihedral pdb=" C TYR G 39 " pdb=" N TYR G 39 " pdb=" CA TYR G 39 " pdb=" CB TYR G 39 " ideal model delta harmonic sigma weight residual -122.60 -132.80 10.20 0 2.50e+00 1.60e-01 1.67e+01 ... (remaining 23205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3297 0.079 - 0.158: 1397 0.158 - 0.237: 467 0.237 - 0.316: 71 0.316 - 0.396: 48 Chirality restraints: 5280 Sorted by residual: chirality pdb=" CA ASN r 50 " pdb=" N ASN r 50 " pdb=" C ASN r 50 " pdb=" CB ASN r 50 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CA ASN H 50 " pdb=" N ASN H 50 " pdb=" C ASN H 50 " pdb=" CB ASN H 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CA ASN 4 50 " pdb=" N ASN 4 50 " pdb=" C ASN 4 50 " pdb=" CB ASN 4 50 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 5277 not shown) Planarity restraints: 6936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 137 " 0.083 2.00e-02 2.50e+03 5.00e-02 5.01e+01 pdb=" CG TYR P 137 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR P 137 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR P 137 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR P 137 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR P 137 " -0.057 2.00e-02 2.50e+03 pdb=" CZ TYR P 137 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR P 137 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 2 137 " -0.083 2.00e-02 2.50e+03 5.00e-02 4.99e+01 pdb=" CG TYR 2 137 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR 2 137 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR 2 137 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR 2 137 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR 2 137 " 0.057 2.00e-02 2.50e+03 pdb=" CZ TYR 2 137 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR 2 137 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 137 " -0.082 2.00e-02 2.50e+03 5.00e-02 4.99e+01 pdb=" CG TYR H 137 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR H 137 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR H 137 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR H 137 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR H 137 " 0.057 2.00e-02 2.50e+03 pdb=" CZ TYR H 137 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYR H 137 " -0.066 2.00e-02 2.50e+03 ... (remaining 6933 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 319 2.41 - 3.03: 28938 3.03 - 3.65: 73590 3.65 - 4.28: 123959 4.28 - 4.90: 189906 Nonbonded interactions: 416712 Sorted by model distance: nonbonded pdb=" OE2 GLU K 101 " pdb=" NH2BARG K 156 " model vdw 1.782 3.120 nonbonded pdb=" OE2 GLU B 101 " pdb=" NH2BARG B 156 " model vdw 1.783 3.120 nonbonded pdb=" OE2 GLU a 101 " pdb=" NH2BARG a 156 " model vdw 1.783 3.120 nonbonded pdb=" OE2 GLU E 101 " pdb=" NH2BARG E 156 " model vdw 1.783 3.120 nonbonded pdb=" OE2 GLU G 101 " pdb=" NH2BARG G 156 " model vdw 1.783 3.120 ... (remaining 416707 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 '1' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain '2' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain '4' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain '6' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'A' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'B' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'E' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'F' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'G' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'H' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'I' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'K' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'M' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 201)) selection = (chain 'O' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'P' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'Q' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'S' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'U' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'W' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'X' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'Y' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'a' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'e' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) selection = (chain 'r' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 63 \ or resid 65 through 67 or resid 69 through 70 or resid 73 through 74 or resid 7 \ 6 through 93 or resid 95 through 108 or resid 110 through 132 or resid 134 throu \ gh 155 or resid 157 through 161 or resid 163 through 171 or resid 173 through 17 \ 6 or resid 300)) } 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=0.50 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.400 Construct map_model_manager: 0.030 Extract box with map and model: 1.500 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 83.470 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 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 : 0.015 0.078 37800 Z= 0.996 Angle : 1.742 8.541 51264 Z= 1.258 Chirality : 0.098 0.396 5280 Planarity : 0.011 0.050 6936 Dihedral : 15.506 80.693 14616 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.66 % Allowed : 3.05 % Favored : 93.29 % Cbeta Deviations : 1.12 % Peptide Plane: Cis-proline : 33.33 % 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: 2.70 (0.11), residues: 4920 helix: 2.12 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.36 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.019 TRP 4 93 HIS 0.019 0.008 HIS a 118 PHE 0.052 0.012 PHE W 41 TYR 0.083 0.020 TYR P 137 ARG 0.022 0.003 ARG G 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 600 time to evaluate : 3.297 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 86 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6545 (mp10) REVERT: A 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6978 (mp0) REVERT: A 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6913 (mttm) REVERT: A 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6715 (mtmt) REVERT: 1 86 GLN cc_start: 0.7350 (mm-40) cc_final: 0.6499 (mp10) REVERT: 1 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6983 (mp0) REVERT: 1 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6915 (mttm) REVERT: 1 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6705 (mtmt) REVERT: K 86 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6460 (mp10) REVERT: K 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6966 (mp0) REVERT: K 143 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6910 (mttm) REVERT: K 157 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6710 (mtmt) REVERT: a 86 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6461 (mp10) REVERT: a 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6956 (mp0) REVERT: a 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6910 (mttm) REVERT: a 157 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6713 (mtmt) REVERT: B 86 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6496 (mp10) REVERT: B 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6972 (mp0) REVERT: B 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6913 (mttm) REVERT: B 157 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6718 (mtmt) REVERT: E 86 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6490 (mp10) REVERT: E 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6973 (mp0) REVERT: E 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6913 (mttm) REVERT: E 157 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6717 (mtmt) REVERT: e 86 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6490 (mp10) REVERT: e 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6979 (mp0) REVERT: e 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6908 (mttm) REVERT: e 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6715 (mtmt) REVERT: r 86 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6495 (mp10) REVERT: r 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6961 (mp0) REVERT: r 143 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6912 (mttm) REVERT: r 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6708 (mtmt) REVERT: G 86 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6498 (mp10) REVERT: G 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6979 (mp0) REVERT: G 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6912 (mttm) REVERT: G 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6704 (mtmt) REVERT: I 86 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6489 (mp10) REVERT: I 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6976 (mp0) REVERT: I 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6911 (mttm) REVERT: I 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6706 (mtmt) REVERT: M 86 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6458 (mp10) REVERT: M 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6975 (mp0) REVERT: M 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6911 (mttm) REVERT: M 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6715 (mtmt) REVERT: O 86 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6495 (mp10) REVERT: O 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6971 (mp0) REVERT: O 143 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6909 (mttm) REVERT: O 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6716 (mtmt) REVERT: Q 86 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6460 (mp10) REVERT: Q 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6980 (mp0) REVERT: Q 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6913 (mttm) REVERT: Q 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6706 (mtmt) REVERT: S 86 GLN cc_start: 0.7329 (mm-40) cc_final: 0.6459 (mp10) REVERT: S 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6966 (mp0) REVERT: S 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6912 (mttm) REVERT: S 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6706 (mtmt) REVERT: U 86 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6495 (mp10) REVERT: U 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6981 (mp0) REVERT: U 143 LYS cc_start: 0.7246 (mtmt) cc_final: 0.6912 (mttm) REVERT: U 157 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6715 (mtmt) REVERT: W 86 GLN cc_start: 0.7329 (mm-40) cc_final: 0.6456 (mp10) REVERT: W 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6966 (mp0) REVERT: W 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6914 (mttm) REVERT: W 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6708 (mtmt) REVERT: Y 86 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6459 (mp10) REVERT: Y 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6971 (mp0) REVERT: Y 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6912 (mttm) REVERT: Y 157 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6717 (mtmt) REVERT: 2 86 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6457 (mp10) REVERT: 2 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6980 (mp0) REVERT: 2 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6911 (mttm) REVERT: 2 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6705 (mtmt) REVERT: 4 86 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6460 (mp10) REVERT: 4 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6975 (mp0) REVERT: 4 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6912 (mttm) REVERT: 4 157 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6710 (mtmt) REVERT: F 86 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6459 (mp10) REVERT: F 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6979 (mp0) REVERT: F 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6908 (mttm) REVERT: F 157 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6714 (mtmt) REVERT: H 86 GLN cc_start: 0.7346 (mm-40) cc_final: 0.6545 (mp10) REVERT: H 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6971 (mp0) REVERT: H 143 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6913 (mttm) REVERT: H 157 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6718 (mtmt) REVERT: P 86 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6463 (mp10) REVERT: P 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6980 (mp0) REVERT: P 143 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6913 (mttm) REVERT: P 157 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6712 (mtmt) REVERT: X 86 GLN cc_start: 0.7333 (mm-40) cc_final: 0.6463 (mp10) REVERT: X 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6972 (mp0) REVERT: X 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6912 (mttm) REVERT: X 157 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6714 (mtmt) REVERT: 6 86 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6491 (mp10) REVERT: 6 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6969 (mp0) REVERT: 6 143 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6913 (mttm) REVERT: 6 157 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6708 (mtmt) outliers start: 48 outliers final: 24 residues processed: 624 average time/residue: 1.5538 time to fit residues: 1148.7479 Evaluate side-chains 496 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 448 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 157 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 157 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 157 LYS Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain r residue 157 LYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 157 LYS Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 157 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain W residue 157 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 157 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 157 LYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain P residue 157 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 157 LYS Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 157 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 238 optimal weight: 1.9990 chunk 370 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 60 HIS A 75 GLN B A 83 GLN A 98 ASN A 112 GLN 1 14 GLN 1 60 HIS 1 75 GLN B 1 83 GLN 1 98 ASN K 14 GLN K 60 HIS K 75 GLN B K 83 GLN K 98 ASN K 112 GLN a 14 GLN a 60 HIS a 75 GLN B a 83 GLN a 98 ASN a 112 GLN B 14 GLN B 60 HIS B 75 GLN B B 83 GLN B 98 ASN E 14 GLN E 60 HIS E 75 GLN B E 83 GLN E 98 ASN e 14 GLN e 60 HIS e 75 GLN B e 83 GLN e 98 ASN e 112 GLN r 14 GLN r 60 HIS r 75 GLN B r 83 GLN r 98 ASN G 14 GLN G 60 HIS G 75 GLN B G 83 GLN G 98 ASN G 112 GLN I 14 GLN I 60 HIS I 75 GLN B I 83 GLN I 98 ASN I 112 GLN M 14 GLN M 60 HIS M 75 GLN B M 83 GLN M 98 ASN M 112 GLN O 14 GLN O 60 HIS O 75 GLN B O 83 GLN O 98 ASN O 112 GLN Q 14 GLN Q 60 HIS Q 75 GLN B Q 83 GLN Q 98 ASN Q 112 GLN S 14 GLN S 60 HIS S 75 GLN B S 83 GLN S 98 ASN S 112 GLN U 14 GLN U 60 HIS U 75 GLN B U 83 GLN U 98 ASN U 112 GLN W 14 GLN W 60 HIS W 75 GLN B W 83 GLN W 98 ASN Y 14 GLN Y 60 HIS Y 75 GLN B Y 83 GLN Y 98 ASN 2 14 GLN 2 60 HIS 2 75 GLN B 2 83 GLN 2 98 ASN 2 112 GLN 4 14 GLN 4 60 HIS 4 75 GLN B 4 83 GLN 4 98 ASN 4 112 GLN F 14 GLN F 60 HIS F 75 GLN B F 83 GLN F 98 ASN F 112 GLN H 14 GLN H 60 HIS H 75 GLN B H 83 GLN H 98 ASN P 14 GLN P 60 HIS P 75 GLN B P 83 GLN P 98 ASN P 112 GLN X 14 GLN X 60 HIS X 75 GLN B X 83 GLN X 98 ASN 6 14 GLN 6 60 HIS 6 75 GLN B 6 83 GLN 6 98 ASN 6 112 GLN Total number of N/Q/H flips: 136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 37800 Z= 0.305 Angle : 0.809 6.241 51264 Z= 0.442 Chirality : 0.043 0.172 5280 Planarity : 0.007 0.087 6936 Dihedral : 7.782 57.691 5304 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.66 % Allowed : 3.66 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.11), residues: 4920 helix: 2.98 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.50 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.005 TRP S 93 HIS 0.009 0.002 HIS 4 60 PHE 0.032 0.004 PHE A 41 TYR 0.023 0.004 TYR A 39 ARG 0.011 0.002 ARG 4 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 457 time to evaluate : 3.308 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: A 86 GLN cc_start: 0.7276 (mm-40) cc_final: 0.6387 (mp10) REVERT: A 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6902 (mp0) REVERT: A 143 LYS cc_start: 0.7268 (mtmt) cc_final: 0.6941 (mttm) REVERT: A 157 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6785 (mmmm) REVERT: 1 86 GLN cc_start: 0.7270 (mm-40) cc_final: 0.6382 (mp10) REVERT: 1 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6839 (mt-10) REVERT: 1 143 LYS cc_start: 0.7279 (mtmt) cc_final: 0.6893 (mttm) REVERT: 1 157 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6782 (mmmm) REVERT: K 86 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6376 (mp10) REVERT: K 140 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6765 (tm-30) REVERT: K 143 LYS cc_start: 0.7269 (mtmt) cc_final: 0.6879 (mttm) REVERT: K 157 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6788 (mmmm) REVERT: a 86 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6369 (mp10) REVERT: a 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6890 (mp0) REVERT: a 143 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6951 (mttm) REVERT: a 157 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6787 (mmmm) REVERT: B 86 GLN cc_start: 0.7272 (mm-40) cc_final: 0.6384 (mp10) REVERT: B 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6906 (mp0) REVERT: B 143 LYS cc_start: 0.7270 (mtmt) cc_final: 0.6944 (mttm) REVERT: B 157 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6813 (mtmt) REVERT: E 86 GLN cc_start: 0.7267 (mm-40) cc_final: 0.6381 (mp10) REVERT: E 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6903 (mp0) REVERT: E 143 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6955 (mttm) REVERT: E 157 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6819 (mtmt) REVERT: e 86 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6387 (mp10) REVERT: e 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6906 (mp0) REVERT: e 143 LYS cc_start: 0.7266 (mtmt) cc_final: 0.6943 (mttm) REVERT: e 157 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6790 (mmmm) REVERT: r 86 GLN cc_start: 0.7278 (mm-40) cc_final: 0.6389 (mp10) REVERT: r 140 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6888 (mp0) REVERT: r 143 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6946 (mttm) REVERT: r 157 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6788 (mmmm) REVERT: G 86 GLN cc_start: 0.7273 (mm-40) cc_final: 0.6383 (mp10) REVERT: G 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6909 (mp0) REVERT: G 143 LYS cc_start: 0.7269 (mtmt) cc_final: 0.6943 (mttm) REVERT: G 157 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6785 (mmmm) REVERT: I 86 GLN cc_start: 0.7269 (mm-40) cc_final: 0.6381 (mp10) REVERT: I 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6907 (mp0) REVERT: I 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6947 (mttm) REVERT: I 157 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6786 (mmmm) REVERT: M 86 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6375 (mp10) REVERT: M 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6926 (mp0) REVERT: M 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6962 (mttm) REVERT: M 157 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6813 (mtmt) REVERT: O 86 GLN cc_start: 0.7281 (mm-40) cc_final: 0.6391 (mp10) REVERT: O 140 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6911 (mp0) REVERT: O 143 LYS cc_start: 0.7269 (mtmt) cc_final: 0.6953 (mttm) REVERT: O 157 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6790 (mmmm) REVERT: Q 86 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6375 (mp10) REVERT: Q 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6906 (mp0) REVERT: Q 143 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6944 (mttm) REVERT: Q 157 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6784 (mmmm) REVERT: S 86 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6370 (mp10) REVERT: S 140 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6904 (mp0) REVERT: S 143 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6947 (mttm) REVERT: S 157 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6788 (mmmm) REVERT: U 86 GLN cc_start: 0.7276 (mm-40) cc_final: 0.6386 (mp10) REVERT: U 140 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6926 (mp0) REVERT: U 143 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6959 (mttm) REVERT: U 157 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6786 (mmmm) REVERT: W 86 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6373 (mp10) REVERT: W 140 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6898 (mp0) REVERT: W 143 LYS cc_start: 0.7268 (mtmt) cc_final: 0.6943 (mttm) REVERT: W 157 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6814 (mtmt) REVERT: Y 86 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6372 (mp10) REVERT: Y 140 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6895 (mp0) REVERT: Y 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6952 (mttm) REVERT: Y 157 LYS cc_start: 0.7211 (OUTLIER) cc_final: 0.6784 (mmmm) REVERT: 2 86 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6374 (mp10) REVERT: 2 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6906 (mp0) REVERT: 2 143 LYS cc_start: 0.7268 (mtmt) cc_final: 0.6938 (mttm) REVERT: 2 157 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6814 (mtmt) REVERT: 4 86 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6376 (mp10) REVERT: 4 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6926 (mp0) REVERT: 4 143 LYS cc_start: 0.7273 (mtmt) cc_final: 0.6956 (mttm) REVERT: 4 157 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6788 (mmmm) REVERT: F 86 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6374 (mp10) REVERT: F 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6905 (mp0) REVERT: F 143 LYS cc_start: 0.7271 (mtmt) cc_final: 0.6944 (mttm) REVERT: F 157 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6816 (mtmt) REVERT: H 86 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6384 (mp10) REVERT: H 140 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6901 (mp0) REVERT: H 143 LYS cc_start: 0.7270 (mtmt) cc_final: 0.6941 (mttm) REVERT: H 157 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6787 (mmmm) REVERT: P 86 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6375 (mp10) REVERT: P 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6902 (mp0) REVERT: P 143 LYS cc_start: 0.7268 (mtmt) cc_final: 0.6938 (mttm) REVERT: P 157 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6786 (mmmm) REVERT: X 86 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6377 (mp10) REVERT: X 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6771 (tm-30) REVERT: X 143 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6886 (mttm) REVERT: X 157 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6786 (mmmm) REVERT: 6 86 GLN cc_start: 0.7273 (mm-40) cc_final: 0.6385 (mp10) REVERT: 6 140 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6772 (tm-30) REVERT: 6 143 LYS cc_start: 0.7270 (mtmt) cc_final: 0.6882 (mttm) REVERT: 6 157 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6780 (mmmm) outliers start: 48 outliers final: 24 residues processed: 481 average time/residue: 1.4284 time to fit residues: 827.4552 Evaluate side-chains 506 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 458 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 157 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 157 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 157 LYS Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain r residue 157 LYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 157 LYS Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 157 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain W residue 157 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 157 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 157 LYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain P residue 157 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 157 LYS Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 157 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 371 optimal weight: 1.9990 chunk 400 optimal weight: 0.7980 chunk 330 optimal weight: 0.9980 chunk 368 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 297 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN K 112 GLN a 112 GLN e 112 GLN G 112 GLN I 112 GLN M 112 GLN O 112 GLN Q 112 GLN S 112 GLN U 112 GLN 2 112 GLN 4 112 GLN F 112 GLN P 112 GLN 6 105 HIS 6 112 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 37800 Z= 0.150 Angle : 0.583 5.181 51264 Z= 0.318 Chirality : 0.036 0.155 5280 Planarity : 0.004 0.027 6936 Dihedral : 7.169 58.661 5304 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.66 % Allowed : 3.66 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.92 (0.12), residues: 4920 helix: 3.77 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.48 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP Q 93 HIS 0.005 0.001 HIS I 60 PHE 0.017 0.002 PHE H 41 TYR 0.018 0.002 TYR 2 39 ARG 0.005 0.001 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 456 time to evaluate : 3.288 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: A 86 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6319 (mp10) REVERT: A 140 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6876 (mp0) REVERT: A 143 LYS cc_start: 0.7261 (mtmt) cc_final: 0.6937 (mttm) REVERT: A 157 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6810 (mtmt) REVERT: 1 86 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6317 (mp10) REVERT: 1 140 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6798 (mt-10) REVERT: 1 143 LYS cc_start: 0.7258 (mtmt) cc_final: 0.6877 (mttm) REVERT: 1 157 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6801 (mtmt) REVERT: K 86 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6345 (mp10) REVERT: K 140 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6866 (mp0) REVERT: K 143 LYS cc_start: 0.7260 (mtmt) cc_final: 0.6937 (mttm) REVERT: K 157 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6804 (mtmt) REVERT: a 86 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6346 (mp10) REVERT: a 140 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6790 (mt-10) REVERT: a 143 LYS cc_start: 0.7259 (mtmt) cc_final: 0.6889 (mttm) REVERT: a 157 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6800 (mtmt) REVERT: B 86 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6322 (mp10) REVERT: B 140 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6758 (mp0) REVERT: B 143 LYS cc_start: 0.7259 (mtmt) cc_final: 0.6879 (mttm) REVERT: B 157 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6794 (mtmt) REVERT: E 86 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6320 (mp10) REVERT: E 140 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6760 (mp0) REVERT: E 143 LYS cc_start: 0.7259 (mtmt) cc_final: 0.6886 (mttm) REVERT: E 157 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6807 (mtmt) REVERT: e 86 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6315 (mp10) REVERT: e 140 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6798 (mt-10) REVERT: e 143 LYS cc_start: 0.7257 (mtmt) cc_final: 0.6885 (mttm) REVERT: e 157 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6805 (mtmt) REVERT: r 86 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6321 (mp10) REVERT: r 140 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6749 (mp0) REVERT: r 143 LYS cc_start: 0.7258 (mtmt) cc_final: 0.6882 (mttm) REVERT: r 157 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6793 (mtmt) REVERT: G 86 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6318 (mp10) REVERT: G 140 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6762 (mp0) REVERT: G 143 LYS cc_start: 0.7259 (mtmt) cc_final: 0.6889 (mttm) REVERT: G 157 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6796 (mtmt) REVERT: I 86 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6314 (mp10) REVERT: I 140 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6883 (mp0) REVERT: I 143 LYS cc_start: 0.7257 (mtmt) cc_final: 0.6933 (mttm) REVERT: I 157 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6792 (mtmt) REVERT: M 86 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6348 (mp10) REVERT: M 140 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6758 (mp0) REVERT: M 143 LYS cc_start: 0.7257 (mtmt) cc_final: 0.6882 (mttm) REVERT: M 157 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6807 (mtmt) REVERT: O 86 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6320 (mp10) REVERT: O 140 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6751 (mp0) REVERT: O 143 LYS cc_start: 0.7258 (mtmt) cc_final: 0.6885 (mttm) REVERT: O 157 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6810 (mtmt) REVERT: Q 86 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6346 (mp10) REVERT: Q 140 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6761 (mp0) REVERT: Q 143 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6885 (mttm) REVERT: Q 157 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6790 (mtmt) REVERT: S 86 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6346 (mp10) REVERT: S 140 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6873 (mp0) REVERT: S 143 LYS cc_start: 0.7257 (mtmt) cc_final: 0.6934 (mttm) REVERT: S 157 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6791 (mtmt) REVERT: U 86 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6318 (mp10) REVERT: U 140 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6881 (mp0) REVERT: U 143 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6936 (mttm) REVERT: U 157 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6804 (mtmt) REVERT: W 86 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6344 (mp10) REVERT: W 140 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6757 (mp0) REVERT: W 143 LYS cc_start: 0.7259 (mtmt) cc_final: 0.6885 (mttm) REVERT: W 157 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6809 (mtmt) REVERT: Y 86 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6344 (mp10) REVERT: Y 140 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6784 (mt-10) REVERT: Y 143 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6889 (mttm) REVERT: Y 157 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6803 (mtmt) REVERT: 2 86 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6344 (mp10) REVERT: 2 140 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6882 (mp0) REVERT: 2 143 LYS cc_start: 0.7258 (mtmt) cc_final: 0.6934 (mttm) REVERT: 2 157 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6791 (mtmt) REVERT: 4 86 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6346 (mp10) REVERT: 4 140 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6879 (mp0) REVERT: 4 143 LYS cc_start: 0.7257 (mtmt) cc_final: 0.6936 (mttm) REVERT: 4 157 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6795 (mtmt) REVERT: F 86 GLN cc_start: 0.7199 (mm-40) cc_final: 0.6345 (mp10) REVERT: F 140 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6880 (mp0) REVERT: F 143 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6936 (mttm) REVERT: F 157 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6797 (mtmt) REVERT: H 86 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6318 (mp10) REVERT: H 140 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6875 (mp0) REVERT: H 143 LYS cc_start: 0.7257 (mtmt) cc_final: 0.6936 (mttm) REVERT: H 157 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6801 (mtmt) REVERT: P 86 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6346 (mp10) REVERT: P 140 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6880 (mp0) REVERT: P 143 LYS cc_start: 0.7256 (mtmt) cc_final: 0.6933 (mttm) REVERT: P 157 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6795 (mtmt) REVERT: X 86 GLN cc_start: 0.7198 (mm-40) cc_final: 0.6346 (mp10) REVERT: X 140 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6880 (mp0) REVERT: X 143 LYS cc_start: 0.7265 (mtmt) cc_final: 0.6941 (mttm) REVERT: X 157 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6791 (mtmt) REVERT: 6 86 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6317 (mp10) REVERT: 6 140 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6868 (mp0) REVERT: 6 143 LYS cc_start: 0.7257 (mtmt) cc_final: 0.6938 (mttm) REVERT: 6 157 LYS cc_start: 0.7220 (OUTLIER) cc_final: 0.6801 (mtmt) outliers start: 48 outliers final: 24 residues processed: 480 average time/residue: 1.4255 time to fit residues: 821.9161 Evaluate side-chains 504 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 456 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 157 LYS Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain K residue 157 LYS Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 157 LYS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 157 LYS Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain r residue 157 LYS Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 157 LYS Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain Q residue 157 LYS Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 157 LYS Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain W residue 157 LYS Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 157 LYS Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 2 residue 157 LYS Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain 4 residue 157 LYS Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 157 LYS Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain P residue 157 LYS Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 157 LYS Chi-restraints excluded: chain 6 residue 117 LEU Chi-restraints excluded: chain 6 residue 157 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 3.9990 chunk 279 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 177 optimal weight: 0.7980 chunk 249 optimal weight: 9.9990 chunk 372 optimal weight: 4.9990 chunk 394 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 353 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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: 0.6913 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 37800 Z= 0.202 Angle : 0.664 5.896 51264 Z= 0.362 Chirality : 0.039 0.155 5280 Planarity : 0.005 0.049 6936 Dihedral : 6.690 44.752 5304 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.05 % Allowed : 4.57 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.63 (0.11), residues: 4920 helix: 3.56 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.46 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP S 93 HIS 0.005 0.001 HIS U 60 PHE 0.022 0.003 PHE E 41 TYR 0.020 0.003 TYR 1 39 ARG 0.004 0.001 ARG P 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 465 time to evaluate : 3.315 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: A 86 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6359 (mp10) REVERT: A 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6913 (mp0) REVERT: A 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6946 (mttm) REVERT: A 157 LYS cc_start: 0.7262 (mttm) cc_final: 0.6842 (mmmm) REVERT: 1 86 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6359 (mp10) REVERT: 1 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6841 (mt-10) REVERT: 1 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6893 (mttm) REVERT: 1 157 LYS cc_start: 0.7268 (mttm) cc_final: 0.6844 (mmmm) REVERT: K 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6381 (mp10) REVERT: K 140 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6909 (mp0) REVERT: K 143 LYS cc_start: 0.7279 (mtmt) cc_final: 0.6953 (mttm) REVERT: K 157 LYS cc_start: 0.7274 (mttm) cc_final: 0.6868 (mmmm) REVERT: a 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6383 (mp10) REVERT: a 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6898 (mp0) REVERT: a 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6946 (mttm) REVERT: a 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6846 (mmmm) REVERT: B 86 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6359 (mp10) REVERT: B 140 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6915 (mp0) REVERT: B 143 LYS cc_start: 0.7282 (mtmt) cc_final: 0.6955 (mttm) REVERT: B 157 LYS cc_start: 0.7259 (mttm) cc_final: 0.6848 (mmmm) REVERT: E 86 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6357 (mp10) REVERT: E 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6903 (mp0) REVERT: E 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6949 (mttm) REVERT: E 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6846 (mmmm) REVERT: e 86 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6358 (mp10) REVERT: e 140 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6905 (mp0) REVERT: e 143 LYS cc_start: 0.7282 (mtmt) cc_final: 0.6943 (mttm) REVERT: e 157 LYS cc_start: 0.7260 (mttm) cc_final: 0.6845 (mmmm) REVERT: r 86 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6361 (mp10) REVERT: r 140 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6900 (mp0) REVERT: r 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6946 (mttm) REVERT: r 157 LYS cc_start: 0.7282 (mttm) cc_final: 0.6851 (mmmm) REVERT: G 86 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6358 (mp10) REVERT: G 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6916 (mp0) REVERT: G 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6948 (mttm) REVERT: G 157 LYS cc_start: 0.7280 (mttm) cc_final: 0.6841 (mmmm) REVERT: I 86 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6357 (mp10) REVERT: I 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6932 (mp0) REVERT: I 143 LYS cc_start: 0.7286 (mtmt) cc_final: 0.6956 (mttm) REVERT: I 157 LYS cc_start: 0.7281 (mttm) cc_final: 0.6845 (mmmm) REVERT: M 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6380 (mp10) REVERT: M 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6917 (mp0) REVERT: M 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6956 (mttm) REVERT: M 157 LYS cc_start: 0.7288 (mttm) cc_final: 0.6849 (mmmm) REVERT: O 86 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6364 (mp10) REVERT: O 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6893 (mp0) REVERT: O 143 LYS cc_start: 0.7287 (mtmt) cc_final: 0.6948 (mttm) REVERT: O 157 LYS cc_start: 0.7266 (mttm) cc_final: 0.6842 (mmmm) REVERT: Q 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6382 (mp10) REVERT: Q 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6915 (mp0) REVERT: Q 143 LYS cc_start: 0.7285 (mtmt) cc_final: 0.6949 (mttm) REVERT: Q 157 LYS cc_start: 0.7285 (mttm) cc_final: 0.6848 (mmmm) REVERT: S 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6382 (mp10) REVERT: S 140 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6914 (mp0) REVERT: S 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6953 (mttm) REVERT: S 157 LYS cc_start: 0.7255 (mttm) cc_final: 0.6841 (mmmm) REVERT: U 86 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6357 (mp10) REVERT: U 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6908 (mp0) REVERT: U 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6948 (mttm) REVERT: U 157 LYS cc_start: 0.7297 (mttm) cc_final: 0.6856 (mmmm) REVERT: W 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6378 (mp10) REVERT: W 140 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6915 (mp0) REVERT: W 143 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6955 (mttm) REVERT: W 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6843 (mmmm) REVERT: Y 86 GLN cc_start: 0.7224 (mm-40) cc_final: 0.6378 (mp10) REVERT: Y 140 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6819 (mt-10) REVERT: Y 143 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6883 (mttm) REVERT: Y 157 LYS cc_start: 0.7268 (mttm) cc_final: 0.6847 (mmmm) REVERT: 2 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6381 (mp10) REVERT: 2 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6917 (mp0) REVERT: 2 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6945 (mttm) REVERT: 2 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6845 (mmmm) REVERT: 4 86 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6380 (mp10) REVERT: 4 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6922 (mp0) REVERT: 4 143 LYS cc_start: 0.7288 (mtmt) cc_final: 0.6959 (mttm) REVERT: 4 157 LYS cc_start: 0.7270 (mttm) cc_final: 0.6843 (mmmm) REVERT: F 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6379 (mp10) REVERT: F 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6933 (mp0) REVERT: F 143 LYS cc_start: 0.7276 (mtmt) cc_final: 0.6950 (mttm) REVERT: F 157 LYS cc_start: 0.7272 (mttm) cc_final: 0.6846 (mmmm) REVERT: H 86 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6356 (mp10) REVERT: H 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6910 (mp0) REVERT: H 143 LYS cc_start: 0.7275 (mtmt) cc_final: 0.6942 (mttm) REVERT: H 157 LYS cc_start: 0.7274 (mttm) cc_final: 0.6850 (mmmm) REVERT: P 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6382 (mp10) REVERT: P 140 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6906 (mp0) REVERT: P 143 LYS cc_start: 0.7283 (mtmt) cc_final: 0.6947 (mttm) REVERT: P 157 LYS cc_start: 0.7269 (mttm) cc_final: 0.6840 (mmmm) REVERT: X 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6381 (mp10) REVERT: X 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6922 (mp0) REVERT: X 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6956 (mttm) REVERT: X 157 LYS cc_start: 0.7290 (mttm) cc_final: 0.6851 (mmmm) REVERT: 6 86 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6359 (mp10) REVERT: 6 140 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6911 (mp0) REVERT: 6 143 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6959 (mttm) REVERT: 6 157 LYS cc_start: 0.7274 (mttm) cc_final: 0.6867 (mmmm) outliers start: 24 outliers final: 24 residues processed: 489 average time/residue: 1.4517 time to fit residues: 850.4301 Evaluate side-chains 480 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 456 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 6.9990 chunk 223 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 336 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 1.9990 chunk 353 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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: 0.6907 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 37800 Z= 0.178 Angle : 0.626 5.594 51264 Z= 0.341 Chirality : 0.037 0.154 5280 Planarity : 0.004 0.037 6936 Dihedral : 5.424 44.588 5208 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.05 % Allowed : 4.37 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.76 (0.12), residues: 4920 helix: 3.65 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.48 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP M 93 HIS 0.004 0.001 HIS M 128 PHE 0.020 0.003 PHE F 41 TYR 0.019 0.002 TYR W 39 ARG 0.003 0.001 ARG H 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 459 time to evaluate : 3.328 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: A 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6348 (mp10) REVERT: A 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6790 (mp0) REVERT: A 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6892 (mttm) REVERT: A 157 LYS cc_start: 0.7266 (mttm) cc_final: 0.6859 (mmmm) REVERT: 1 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6342 (mp10) REVERT: 1 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6788 (mp0) REVERT: 1 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6903 (mttm) REVERT: 1 157 LYS cc_start: 0.7274 (mttm) cc_final: 0.6859 (mmmm) REVERT: K 86 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6375 (mp10) REVERT: K 140 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6780 (mp0) REVERT: K 143 LYS cc_start: 0.7291 (mtmt) cc_final: 0.6892 (mttm) REVERT: K 157 LYS cc_start: 0.7281 (mttm) cc_final: 0.6878 (mmmm) REVERT: a 86 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6372 (mp10) REVERT: a 140 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6781 (mp0) REVERT: a 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6901 (mttm) REVERT: a 157 LYS cc_start: 0.7296 (mttm) cc_final: 0.6863 (mmmm) REVERT: B 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6346 (mp10) REVERT: B 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6786 (mp0) REVERT: B 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6902 (mttm) REVERT: B 157 LYS cc_start: 0.7266 (mttm) cc_final: 0.6863 (mmmm) REVERT: E 86 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6346 (mp10) REVERT: E 140 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6785 (mp0) REVERT: E 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6903 (mttm) REVERT: E 157 LYS cc_start: 0.7293 (mttm) cc_final: 0.6860 (mmmm) REVERT: e 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6346 (mp10) REVERT: e 140 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6788 (mp0) REVERT: e 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6899 (mttm) REVERT: e 157 LYS cc_start: 0.7272 (mttm) cc_final: 0.6870 (mmmm) REVERT: r 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6350 (mp10) REVERT: r 140 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6782 (mp0) REVERT: r 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6900 (mttm) REVERT: r 157 LYS cc_start: 0.7297 (mttm) cc_final: 0.6863 (mmmm) REVERT: G 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6346 (mp10) REVERT: G 140 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6789 (mp0) REVERT: G 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6895 (mttm) REVERT: G 157 LYS cc_start: 0.7297 (mttm) cc_final: 0.6862 (mmmm) REVERT: I 86 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6345 (mp10) REVERT: I 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6795 (mp0) REVERT: I 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6900 (mttm) REVERT: I 157 LYS cc_start: 0.7293 (mttm) cc_final: 0.6858 (mmmm) REVERT: M 86 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6377 (mp10) REVERT: M 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6781 (mp0) REVERT: M 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6902 (mttm) REVERT: M 157 LYS cc_start: 0.7294 (mttm) cc_final: 0.6860 (mmmm) REVERT: O 86 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6356 (mp10) REVERT: O 140 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6778 (mp0) REVERT: O 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6900 (mttm) REVERT: O 157 LYS cc_start: 0.7271 (mttm) cc_final: 0.6866 (mmmm) REVERT: Q 86 GLN cc_start: 0.7218 (mm-40) cc_final: 0.6375 (mp10) REVERT: Q 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6787 (mp0) REVERT: Q 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6895 (mttm) REVERT: Q 157 LYS cc_start: 0.7294 (mttm) cc_final: 0.6860 (mmmm) REVERT: S 86 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6377 (mp10) REVERT: S 140 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6783 (mp0) REVERT: S 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6902 (mttm) REVERT: S 157 LYS cc_start: 0.7270 (mttm) cc_final: 0.6866 (mmmm) REVERT: U 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6346 (mp10) REVERT: U 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6787 (mp0) REVERT: U 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6899 (mttm) REVERT: U 157 LYS cc_start: 0.7298 (mttm) cc_final: 0.6862 (mmmm) REVERT: W 86 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6374 (mp10) REVERT: W 140 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6785 (mp0) REVERT: W 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6895 (mttm) REVERT: W 157 LYS cc_start: 0.7279 (mttm) cc_final: 0.6862 (mmmm) REVERT: Y 86 GLN cc_start: 0.7214 (mm-40) cc_final: 0.6372 (mp10) REVERT: Y 140 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6779 (mp0) REVERT: Y 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6896 (mttm) REVERT: Y 157 LYS cc_start: 0.7261 (mttm) cc_final: 0.6859 (mmmm) REVERT: 2 86 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6374 (mp10) REVERT: 2 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6788 (mp0) REVERT: 2 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6893 (mttm) REVERT: 2 157 LYS cc_start: 0.7299 (mttm) cc_final: 0.6865 (mmmm) REVERT: 4 86 GLN cc_start: 0.7217 (mm-40) cc_final: 0.6375 (mp10) REVERT: 4 140 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6790 (mp0) REVERT: 4 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6901 (mttm) REVERT: 4 157 LYS cc_start: 0.7271 (mttm) cc_final: 0.6859 (mmmm) REVERT: F 86 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6376 (mp10) REVERT: F 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6788 (mp0) REVERT: F 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6893 (mttm) REVERT: F 157 LYS cc_start: 0.7266 (mttm) cc_final: 0.6863 (mmmm) REVERT: H 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6345 (mp10) REVERT: H 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6790 (mp0) REVERT: H 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6895 (mttm) REVERT: H 157 LYS cc_start: 0.7277 (mttm) cc_final: 0.6863 (mmmm) REVERT: P 86 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6376 (mp10) REVERT: P 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6787 (mp0) REVERT: P 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6893 (mttm) REVERT: P 157 LYS cc_start: 0.7271 (mttm) cc_final: 0.6858 (mmmm) REVERT: X 86 GLN cc_start: 0.7223 (mm-40) cc_final: 0.6378 (mp10) REVERT: X 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6805 (mp0) REVERT: X 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6901 (mttm) REVERT: X 157 LYS cc_start: 0.7280 (mttm) cc_final: 0.6857 (mmmm) REVERT: 6 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6342 (mp10) REVERT: 6 140 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6779 (mp0) REVERT: 6 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6901 (mttm) REVERT: 6 157 LYS cc_start: 0.7272 (mttm) cc_final: 0.6869 (mmmm) outliers start: 24 outliers final: 24 residues processed: 483 average time/residue: 1.4467 time to fit residues: 839.0335 Evaluate side-chains 480 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 456 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 5.9990 chunk 355 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 394 optimal weight: 10.0000 chunk 327 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.6919 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 37800 Z= 0.236 Angle : 0.703 6.193 51264 Z= 0.383 Chirality : 0.040 0.155 5280 Planarity : 0.005 0.060 6936 Dihedral : 5.517 44.935 5208 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.05 % Allowed : 3.89 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.47 (0.11), residues: 4920 helix: 3.43 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.48 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP K 93 HIS 0.007 0.001 HIS M 60 PHE 0.025 0.004 PHE W 41 TYR 0.023 0.003 TYR I 39 ARG 0.004 0.001 ARG B 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 457 time to evaluate : 3.353 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: A 86 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6370 (mp10) REVERT: A 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6921 (mp0) REVERT: A 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6963 (mttm) REVERT: A 157 LYS cc_start: 0.7265 (mttm) cc_final: 0.6861 (mmmm) REVERT: 1 86 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6372 (mp10) REVERT: 1 140 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6923 (mp0) REVERT: 1 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6964 (mttm) REVERT: 1 157 LYS cc_start: 0.7274 (mttm) cc_final: 0.6866 (mmmm) REVERT: K 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6393 (mp10) REVERT: K 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6801 (mp0) REVERT: K 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6903 (mttm) REVERT: K 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6877 (mmmm) REVERT: a 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6389 (mp10) REVERT: a 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6800 (mp0) REVERT: a 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6902 (mttm) REVERT: a 157 LYS cc_start: 0.7300 (mttm) cc_final: 0.6859 (mmmm) REVERT: B 86 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6373 (mp10) REVERT: B 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6920 (mp0) REVERT: B 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6966 (mttm) REVERT: B 157 LYS cc_start: 0.7277 (mttm) cc_final: 0.6868 (mmmm) REVERT: E 86 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6374 (mp10) REVERT: E 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6919 (mp0) REVERT: E 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6965 (mttm) REVERT: E 157 LYS cc_start: 0.7293 (mttm) cc_final: 0.6862 (mmmm) REVERT: e 86 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6370 (mp10) REVERT: e 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6921 (mp0) REVERT: e 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6962 (mttm) REVERT: e 157 LYS cc_start: 0.7280 (mttm) cc_final: 0.6872 (mmmm) REVERT: r 86 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6373 (mp10) REVERT: r 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6799 (mp0) REVERT: r 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6902 (mttm) REVERT: r 157 LYS cc_start: 0.7301 (mttm) cc_final: 0.6859 (mmmm) REVERT: G 86 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6373 (mp10) REVERT: G 140 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6923 (mp0) REVERT: G 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6965 (mttm) REVERT: G 157 LYS cc_start: 0.7307 (mttm) cc_final: 0.6865 (mmmm) REVERT: I 86 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6373 (mp10) REVERT: I 140 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6926 (mp0) REVERT: I 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6964 (mttm) REVERT: I 157 LYS cc_start: 0.7297 (mttm) cc_final: 0.6856 (mmmm) REVERT: M 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6391 (mp10) REVERT: M 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6918 (mp0) REVERT: M 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6966 (mttm) REVERT: M 157 LYS cc_start: 0.7287 (mttm) cc_final: 0.6861 (mmmm) REVERT: O 86 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6377 (mp10) REVERT: O 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6797 (mp0) REVERT: O 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6902 (mttm) REVERT: O 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6861 (mmmm) REVERT: Q 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6388 (mp10) REVERT: Q 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6916 (mp0) REVERT: Q 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6963 (mttm) REVERT: Q 157 LYS cc_start: 0.7299 (mttm) cc_final: 0.6859 (mmmm) REVERT: S 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6387 (mp10) REVERT: S 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6914 (mp0) REVERT: S 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6964 (mttm) REVERT: S 157 LYS cc_start: 0.7273 (mttm) cc_final: 0.6866 (mmmm) REVERT: U 86 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6371 (mp10) REVERT: U 140 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6926 (mp0) REVERT: U 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6963 (mttm) REVERT: U 157 LYS cc_start: 0.7305 (mttm) cc_final: 0.6861 (mmmm) REVERT: W 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6389 (mp10) REVERT: W 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6916 (mp0) REVERT: W 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6965 (mttm) REVERT: W 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6859 (mmmm) REVERT: Y 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6390 (mp10) REVERT: Y 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6910 (mp0) REVERT: Y 143 LYS cc_start: 0.7302 (mtmt) cc_final: 0.6965 (mttm) REVERT: Y 157 LYS cc_start: 0.7277 (mttm) cc_final: 0.6871 (mmmm) REVERT: 2 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6388 (mp10) REVERT: 2 140 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6924 (mp0) REVERT: 2 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6961 (mttm) REVERT: 2 157 LYS cc_start: 0.7299 (mttm) cc_final: 0.6856 (mmmm) REVERT: 4 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6390 (mp10) REVERT: 4 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6925 (mp0) REVERT: 4 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6965 (mttm) REVERT: 4 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6861 (mmmm) REVERT: F 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6386 (mp10) REVERT: F 140 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6922 (mp0) REVERT: F 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6965 (mttm) REVERT: F 157 LYS cc_start: 0.7271 (mttm) cc_final: 0.6864 (mmmm) REVERT: H 86 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6370 (mp10) REVERT: H 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6809 (mp0) REVERT: H 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6905 (mttm) REVERT: H 157 LYS cc_start: 0.7273 (mttm) cc_final: 0.6866 (mmmm) REVERT: P 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6389 (mp10) REVERT: P 140 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6922 (mp0) REVERT: P 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6964 (mttm) REVERT: P 157 LYS cc_start: 0.7276 (mttm) cc_final: 0.6852 (mmmm) REVERT: X 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6391 (mp10) REVERT: X 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6925 (mp0) REVERT: X 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6965 (mttm) REVERT: X 157 LYS cc_start: 0.7282 (mttm) cc_final: 0.6858 (mmmm) REVERT: 6 86 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6374 (mp10) REVERT: 6 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6906 (mp0) REVERT: 6 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6964 (mttm) REVERT: 6 157 LYS cc_start: 0.7284 (mttm) cc_final: 0.6878 (mmmm) outliers start: 24 outliers final: 24 residues processed: 481 average time/residue: 1.4467 time to fit residues: 835.1183 Evaluate side-chains 480 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 456 time to evaluate : 3.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 393 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 239 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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: 0.6914 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 37800 Z= 0.208 Angle : 0.667 5.880 51264 Z= 0.363 Chirality : 0.038 0.155 5280 Planarity : 0.005 0.050 6936 Dihedral : 5.480 44.744 5208 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.05 % Allowed : 4.27 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.57 (0.11), residues: 4920 helix: 3.50 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.50 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP Y 93 HIS 0.004 0.001 HIS E 128 PHE 0.023 0.003 PHE F 41 TYR 0.022 0.002 TYR U 39 ARG 0.004 0.001 ARG 6 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 459 time to evaluate : 3.300 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: A 86 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6359 (mp10) REVERT: A 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6802 (mp0) REVERT: A 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6906 (mttm) REVERT: A 157 LYS cc_start: 0.7268 (mttm) cc_final: 0.6865 (mmmm) REVERT: 1 86 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6360 (mp10) REVERT: 1 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6801 (mp0) REVERT: 1 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6913 (mttm) REVERT: 1 157 LYS cc_start: 0.7270 (mttm) cc_final: 0.6864 (mmmm) REVERT: K 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6393 (mp10) REVERT: K 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6792 (mp0) REVERT: K 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6906 (mttm) REVERT: K 157 LYS cc_start: 0.7280 (mttm) cc_final: 0.6875 (mmmm) REVERT: a 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6389 (mp10) REVERT: a 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6798 (mp0) REVERT: a 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6909 (mttm) REVERT: a 157 LYS cc_start: 0.7287 (mttm) cc_final: 0.6853 (mmmm) REVERT: B 86 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6361 (mp10) REVERT: B 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6802 (mp0) REVERT: B 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6914 (mttm) REVERT: B 157 LYS cc_start: 0.7263 (mttm) cc_final: 0.6862 (mmmm) REVERT: E 86 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6364 (mp10) REVERT: E 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6799 (mp0) REVERT: E 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6913 (mttm) REVERT: E 157 LYS cc_start: 0.7281 (mttm) cc_final: 0.6856 (mmmm) REVERT: e 86 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6360 (mp10) REVERT: e 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6800 (mp0) REVERT: e 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6908 (mttm) REVERT: e 157 LYS cc_start: 0.7269 (mttm) cc_final: 0.6864 (mmmm) REVERT: r 86 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6360 (mp10) REVERT: r 140 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6796 (mp0) REVERT: r 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6910 (mttm) REVERT: r 157 LYS cc_start: 0.7300 (mttm) cc_final: 0.6860 (mmmm) REVERT: G 86 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6362 (mp10) REVERT: G 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6804 (mp0) REVERT: G 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6912 (mttm) REVERT: G 157 LYS cc_start: 0.7295 (mttm) cc_final: 0.6854 (mmmm) REVERT: I 86 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6363 (mp10) REVERT: I 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6807 (mp0) REVERT: I 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6911 (mttm) REVERT: I 157 LYS cc_start: 0.7299 (mttm) cc_final: 0.6859 (mmmm) REVERT: M 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6394 (mp10) REVERT: M 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6798 (mp0) REVERT: M 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6912 (mttm) REVERT: M 157 LYS cc_start: 0.7281 (mttm) cc_final: 0.6854 (mmmm) REVERT: O 86 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6364 (mp10) REVERT: O 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6791 (mp0) REVERT: O 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6908 (mttm) REVERT: O 157 LYS cc_start: 0.7277 (mttm) cc_final: 0.6858 (mmmm) REVERT: Q 86 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6396 (mp10) REVERT: Q 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6913 (mp0) REVERT: Q 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6972 (mttm) REVERT: Q 157 LYS cc_start: 0.7299 (mttm) cc_final: 0.6860 (mmmm) REVERT: S 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6390 (mp10) REVERT: S 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6797 (mp0) REVERT: S 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6912 (mttm) REVERT: S 157 LYS cc_start: 0.7266 (mttm) cc_final: 0.6861 (mmmm) REVERT: U 86 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6363 (mp10) REVERT: U 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6802 (mp0) REVERT: U 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6910 (mttm) REVERT: U 157 LYS cc_start: 0.7295 (mttm) cc_final: 0.6851 (mmmm) REVERT: W 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6391 (mp10) REVERT: W 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6802 (mp0) REVERT: W 143 LYS cc_start: 0.7302 (mtmt) cc_final: 0.6910 (mttm) REVERT: W 157 LYS cc_start: 0.7276 (mttm) cc_final: 0.6855 (mmmm) REVERT: Y 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6393 (mp10) REVERT: Y 140 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6789 (mp0) REVERT: Y 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6903 (mttm) REVERT: Y 157 LYS cc_start: 0.7270 (mttm) cc_final: 0.6868 (mmmm) REVERT: 2 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6391 (mp10) REVERT: 2 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6806 (mp0) REVERT: 2 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6905 (mttm) REVERT: 2 157 LYS cc_start: 0.7289 (mttm) cc_final: 0.6848 (mmmm) REVERT: 4 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6394 (mp10) REVERT: 4 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6801 (mp0) REVERT: 4 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6912 (mttm) REVERT: 4 157 LYS cc_start: 0.7275 (mttm) cc_final: 0.6862 (mmmm) REVERT: F 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6388 (mp10) REVERT: F 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6919 (mp0) REVERT: F 143 LYS cc_start: 0.7302 (mtmt) cc_final: 0.6969 (mttm) REVERT: F 157 LYS cc_start: 0.7263 (mttm) cc_final: 0.6858 (mmmm) REVERT: H 86 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6360 (mp10) REVERT: H 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6807 (mp0) REVERT: H 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6908 (mttm) REVERT: H 157 LYS cc_start: 0.7266 (mttm) cc_final: 0.6863 (mmmm) REVERT: P 86 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6395 (mp10) REVERT: P 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6804 (mp0) REVERT: P 143 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6907 (mttm) REVERT: P 157 LYS cc_start: 0.7277 (mttm) cc_final: 0.6855 (mmmm) REVERT: X 86 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6394 (mp10) REVERT: X 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6802 (mp0) REVERT: X 143 LYS cc_start: 0.7302 (mtmt) cc_final: 0.6914 (mttm) REVERT: X 157 LYS cc_start: 0.7278 (mttm) cc_final: 0.6855 (mmmm) REVERT: 6 86 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6367 (mp10) REVERT: 6 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6792 (mp0) REVERT: 6 143 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6912 (mttm) REVERT: 6 157 LYS cc_start: 0.7271 (mttm) cc_final: 0.6868 (mmmm) outliers start: 24 outliers final: 24 residues processed: 483 average time/residue: 1.4087 time to fit residues: 818.0153 Evaluate side-chains 480 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 456 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.6915 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 37800 Z= 0.210 Angle : 0.675 6.463 51264 Z= 0.368 Chirality : 0.039 0.155 5280 Planarity : 0.005 0.052 6936 Dihedral : 5.481 44.793 5208 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.02 % Allowed : 4.50 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.57 (0.11), residues: 4920 helix: 3.50 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.50 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP Y 93 HIS 0.004 0.001 HIS 2 128 PHE 0.023 0.003 PHE U 41 TYR 0.022 0.003 TYR W 39 ARG 0.004 0.001 ARG r 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 465 time to evaluate : 3.794 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: A 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6358 (mp10) REVERT: A 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6803 (mp0) REVERT: A 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6910 (mttm) REVERT: A 157 LYS cc_start: 0.7268 (mttm) cc_final: 0.6865 (mmmm) REVERT: 1 86 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6370 (mp10) REVERT: 1 140 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6800 (mp0) REVERT: 1 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6912 (mttm) REVERT: 1 157 LYS cc_start: 0.7271 (mttm) cc_final: 0.6863 (mmmm) REVERT: K 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6389 (mp10) REVERT: K 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6792 (mp0) REVERT: K 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6910 (mttm) REVERT: K 157 LYS cc_start: 0.7276 (mttm) cc_final: 0.6872 (mmmm) REVERT: a 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6394 (mp10) REVERT: a 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6799 (mp0) REVERT: a 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6910 (mttm) REVERT: a 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6860 (mmmm) REVERT: B 86 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6364 (mp10) REVERT: B 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6803 (mp0) REVERT: B 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6911 (mttm) REVERT: B 157 LYS cc_start: 0.7268 (mttm) cc_final: 0.6866 (mmmm) REVERT: E 86 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6370 (mp10) REVERT: E 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6798 (mp0) REVERT: E 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6910 (mttm) REVERT: E 157 LYS cc_start: 0.7277 (mttm) cc_final: 0.6852 (mmmm) REVERT: e 86 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6360 (mp10) REVERT: e 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6800 (mp0) REVERT: e 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6907 (mttm) REVERT: e 157 LYS cc_start: 0.7265 (mttm) cc_final: 0.6862 (mmmm) REVERT: r 86 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6360 (mp10) REVERT: r 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6796 (mp0) REVERT: r 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6910 (mttm) REVERT: r 157 LYS cc_start: 0.7298 (mttm) cc_final: 0.6855 (mmmm) REVERT: G 86 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6365 (mp10) REVERT: G 140 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6802 (mp0) REVERT: G 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6910 (mttm) REVERT: G 157 LYS cc_start: 0.7303 (mttm) cc_final: 0.6861 (mmmm) REVERT: I 86 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6363 (mp10) REVERT: I 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6923 (mp0) REVERT: I 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6971 (mttm) REVERT: I 157 LYS cc_start: 0.7304 (mttm) cc_final: 0.6862 (mmmm) REVERT: M 86 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6386 (mp10) REVERT: M 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6799 (mp0) REVERT: M 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6909 (mttm) REVERT: M 157 LYS cc_start: 0.7278 (mttm) cc_final: 0.6854 (mmmm) REVERT: O 86 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6368 (mp10) REVERT: O 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6791 (mp0) REVERT: O 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6908 (mttm) REVERT: O 157 LYS cc_start: 0.7281 (mttm) cc_final: 0.6861 (mmmm) REVERT: Q 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6390 (mp10) REVERT: Q 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6913 (mp0) REVERT: Q 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6971 (mttm) REVERT: Q 157 LYS cc_start: 0.7293 (mttm) cc_final: 0.6853 (mmmm) REVERT: S 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6393 (mp10) REVERT: S 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6797 (mp0) REVERT: S 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6910 (mttm) REVERT: S 157 LYS cc_start: 0.7267 (mttm) cc_final: 0.6863 (mmmm) REVERT: U 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6362 (mp10) REVERT: U 140 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6802 (mp0) REVERT: U 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6908 (mttm) REVERT: U 157 LYS cc_start: 0.7290 (mttm) cc_final: 0.6847 (mmmm) REVERT: W 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6389 (mp10) REVERT: W 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6798 (mp0) REVERT: W 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6911 (mttm) REVERT: W 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6860 (mmmm) REVERT: Y 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6390 (mp10) REVERT: Y 140 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6790 (mp0) REVERT: Y 143 LYS cc_start: 0.7303 (mtmt) cc_final: 0.6909 (mttm) REVERT: Y 157 LYS cc_start: 0.7273 (mttm) cc_final: 0.6868 (mmmm) REVERT: 2 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6390 (mp10) REVERT: 2 140 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6801 (mp0) REVERT: 2 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6908 (mttm) REVERT: 2 157 LYS cc_start: 0.7294 (mttm) cc_final: 0.6851 (mmmm) REVERT: 4 86 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6396 (mp10) REVERT: 4 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6801 (mp0) REVERT: 4 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6910 (mttm) REVERT: 4 157 LYS cc_start: 0.7275 (mttm) cc_final: 0.6860 (mmmm) REVERT: F 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6389 (mp10) REVERT: F 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6915 (mp0) REVERT: F 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6971 (mttm) REVERT: F 157 LYS cc_start: 0.7268 (mttm) cc_final: 0.6862 (mmmm) REVERT: H 86 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6362 (mp10) REVERT: H 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6807 (mp0) REVERT: H 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6910 (mttm) REVERT: H 157 LYS cc_start: 0.7265 (mttm) cc_final: 0.6861 (mmmm) REVERT: P 86 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6393 (mp10) REVERT: P 140 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6800 (mp0) REVERT: P 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6911 (mttm) REVERT: P 157 LYS cc_start: 0.7284 (mttm) cc_final: 0.6861 (mmmm) REVERT: X 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6390 (mp10) REVERT: X 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6802 (mp0) REVERT: X 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6910 (mttm) REVERT: X 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6859 (mmmm) REVERT: 6 86 GLN cc_start: 0.7239 (mm-40) cc_final: 0.6367 (mp10) REVERT: 6 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6792 (mp0) REVERT: 6 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6909 (mttm) REVERT: 6 157 LYS cc_start: 0.7274 (mttm) cc_final: 0.6871 (mmmm) outliers start: 24 outliers final: 24 residues processed: 489 average time/residue: 1.5023 time to fit residues: 882.5558 Evaluate side-chains 480 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 456 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 9.9990 chunk 376 optimal weight: 4.9990 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 287 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 chunk 346 optimal weight: 5.9990 chunk 365 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN 1 139 ASN K 139 ASN a 139 ASN B 139 ASN E 139 ASN e 139 ASN r 139 ASN G 139 ASN I 139 ASN M 139 ASN O 139 ASN Q 139 ASN S 139 ASN U 139 ASN W 139 ASN Y 139 ASN 2 139 ASN 4 139 ASN F 139 ASN H 139 ASN P 139 ASN X 139 ASN 6 139 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 37800 Z= 0.240 Angle : 0.713 6.266 51264 Z= 0.389 Chirality : 0.040 0.156 5280 Planarity : 0.006 0.073 6936 Dihedral : 5.528 44.932 5208 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.02 % Allowed : 4.27 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.45 (0.11), residues: 4920 helix: 3.41 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.50 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.004 TRP K 93 HIS 0.005 0.001 HIS B 60 PHE 0.026 0.004 PHE F 41 TYR 0.023 0.003 TYR K 39 ARG 0.006 0.001 ARG O 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 456 time to evaluate : 4.363 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: A 86 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6376 (mp10) REVERT: A 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6914 (mp0) REVERT: A 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6970 (mttm) REVERT: A 157 LYS cc_start: 0.7272 (mttm) cc_final: 0.6865 (mmmm) REVERT: 1 86 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6378 (mp10) REVERT: 1 140 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6801 (mp0) REVERT: 1 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6912 (mttm) REVERT: 1 157 LYS cc_start: 0.7272 (mttm) cc_final: 0.6862 (mmmm) REVERT: K 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6388 (mp10) REVERT: K 140 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6798 (mp0) REVERT: K 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6904 (mttm) REVERT: K 157 LYS cc_start: 0.7277 (mttm) cc_final: 0.6869 (mmmm) REVERT: a 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6390 (mp10) REVERT: a 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6796 (mp0) REVERT: a 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6908 (mttm) REVERT: a 157 LYS cc_start: 0.7298 (mttm) cc_final: 0.6854 (mmmm) REVERT: B 86 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6377 (mp10) REVERT: B 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6914 (mp0) REVERT: B 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6972 (mttm) REVERT: B 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6877 (mtmt) REVERT: E 86 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6382 (mp10) REVERT: E 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6914 (mp0) REVERT: E 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6968 (mttm) REVERT: E 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6856 (mmmm) REVERT: e 86 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6376 (mp10) REVERT: e 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6916 (mp0) REVERT: e 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6970 (mttm) REVERT: e 157 LYS cc_start: 0.7270 (mttm) cc_final: 0.6863 (mmmm) REVERT: r 86 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6378 (mp10) REVERT: r 140 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6796 (mp0) REVERT: r 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6909 (mttm) REVERT: r 157 LYS cc_start: 0.7296 (mttm) cc_final: 0.6852 (mmmm) REVERT: G 86 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6378 (mp10) REVERT: G 140 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6920 (mp0) REVERT: G 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6971 (mttm) REVERT: G 157 LYS cc_start: 0.7302 (mttm) cc_final: 0.6858 (mmmm) REVERT: I 86 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6379 (mp10) REVERT: I 140 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6926 (mp0) REVERT: I 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6970 (mttm) REVERT: I 157 LYS cc_start: 0.7297 (mttm) cc_final: 0.6854 (mmmm) REVERT: M 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6390 (mp10) REVERT: M 140 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6917 (mp0) REVERT: M 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6967 (mttm) REVERT: M 157 LYS cc_start: 0.7285 (mttm) cc_final: 0.6857 (mmmm) REVERT: O 86 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6379 (mp10) REVERT: O 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6795 (mp0) REVERT: O 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6909 (mttm) REVERT: O 157 LYS cc_start: 0.7285 (mttm) cc_final: 0.6861 (mmmm) REVERT: Q 86 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6394 (mp10) REVERT: Q 140 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6917 (mp0) REVERT: Q 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6972 (mttm) REVERT: Q 157 LYS cc_start: 0.7296 (mttm) cc_final: 0.6853 (mmmm) REVERT: S 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6388 (mp10) REVERT: S 140 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6912 (mp0) REVERT: S 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6971 (mttm) REVERT: S 157 LYS cc_start: 0.7273 (mttm) cc_final: 0.6864 (mmmm) REVERT: U 86 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6377 (mp10) REVERT: U 140 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6804 (mp0) REVERT: U 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6904 (mttm) REVERT: U 157 LYS cc_start: 0.7289 (mttm) cc_final: 0.6844 (mmmm) REVERT: W 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6387 (mp10) REVERT: W 140 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6913 (mp0) REVERT: W 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6972 (mttm) REVERT: W 157 LYS cc_start: 0.7284 (mttm) cc_final: 0.6857 (mmmm) REVERT: Y 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6391 (mp10) REVERT: Y 140 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6905 (mp0) REVERT: Y 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6965 (mttm) REVERT: Y 157 LYS cc_start: 0.7271 (mttm) cc_final: 0.6864 (mmmm) REVERT: 2 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6389 (mp10) REVERT: 2 140 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6919 (mp0) REVERT: 2 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6965 (mttm) REVERT: 2 157 LYS cc_start: 0.7300 (mttm) cc_final: 0.6856 (mmmm) REVERT: 4 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6389 (mp10) REVERT: 4 140 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6807 (mp0) REVERT: 4 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6904 (mttm) REVERT: 4 157 LYS cc_start: 0.7284 (mttm) cc_final: 0.6859 (mmmm) REVERT: F 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6390 (mp10) REVERT: F 140 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6918 (mp0) REVERT: F 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6965 (mttm) REVERT: F 157 LYS cc_start: 0.7270 (mttm) cc_final: 0.6862 (mmmm) REVERT: H 86 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6376 (mp10) REVERT: H 140 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6804 (mp0) REVERT: H 143 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6907 (mttm) REVERT: H 157 LYS cc_start: 0.7273 (mttm) cc_final: 0.6864 (mmmm) REVERT: P 86 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6393 (mp10) REVERT: P 140 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6919 (mp0) REVERT: P 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6966 (mttm) REVERT: P 157 LYS cc_start: 0.7284 (mttm) cc_final: 0.6858 (mmmm) REVERT: X 86 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6392 (mp10) REVERT: X 140 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6806 (mp0) REVERT: X 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6906 (mttm) REVERT: X 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6856 (mmmm) REVERT: 6 86 GLN cc_start: 0.7246 (mm-40) cc_final: 0.6381 (mp10) REVERT: 6 140 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6793 (mp0) REVERT: 6 143 LYS cc_start: 0.7297 (mtmt) cc_final: 0.6909 (mttm) REVERT: 6 157 LYS cc_start: 0.7278 (mttm) cc_final: 0.6871 (mmmm) outliers start: 24 outliers final: 24 residues processed: 480 average time/residue: 1.4775 time to fit residues: 851.7437 Evaluate side-chains 480 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 456 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 3.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 0.0770 chunk 183 optimal weight: 0.9980 chunk 269 optimal weight: 1.9990 chunk 406 optimal weight: 5.9990 chunk 374 optimal weight: 6.9990 chunk 323 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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: 0.6910 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 37800 Z= 0.194 Angle : 0.661 7.627 51264 Z= 0.360 Chirality : 0.038 0.156 5280 Planarity : 0.005 0.073 6936 Dihedral : 5.462 44.588 5208 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.02 % Allowed : 4.27 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.69 (0.11), residues: 4920 helix: 3.59 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.52 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP Q 93 HIS 0.008 0.001 HIS A 60 PHE 0.022 0.003 PHE F 41 TYR 0.020 0.002 TYR P 39 ARG 0.007 0.001 ARG M 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9840 Ramachandran restraints generated. 4920 Oldfield, 0 Emsley, 4920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 459 time to evaluate : 4.183 Fit side-chains REVERT: A 63 ARG cc_start: 0.7063 (ttp-170) cc_final: 0.6791 (tpt-90) REVERT: A 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6354 (mp10) REVERT: A 140 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6787 (mp0) REVERT: A 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6905 (mttm) REVERT: A 157 LYS cc_start: 0.7265 (mttm) cc_final: 0.6857 (mmmm) REVERT: 1 63 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.6816 (tpt-90) REVERT: 1 86 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6357 (mp10) REVERT: 1 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6786 (mp0) REVERT: 1 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6910 (mttm) REVERT: 1 157 LYS cc_start: 0.7256 (mttm) cc_final: 0.6853 (mmmm) REVERT: K 63 ARG cc_start: 0.7077 (ttp-170) cc_final: 0.6823 (tpt-90) REVERT: K 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6390 (mp10) REVERT: K 140 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6779 (mp0) REVERT: K 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6906 (mttm) REVERT: K 157 LYS cc_start: 0.7272 (mttm) cc_final: 0.6872 (mmmm) REVERT: a 63 ARG cc_start: 0.7061 (ttp-170) cc_final: 0.6819 (tpt-90) REVERT: a 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6391 (mp10) REVERT: a 140 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6783 (mp0) REVERT: a 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6907 (mttm) REVERT: a 157 LYS cc_start: 0.7265 (mttm) cc_final: 0.6841 (mmmm) REVERT: B 63 ARG cc_start: 0.7082 (ttp-170) cc_final: 0.6826 (tpt-90) REVERT: B 86 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6357 (mp10) REVERT: B 140 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6789 (mp0) REVERT: B 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6909 (mttm) REVERT: B 157 LYS cc_start: 0.7268 (mttm) cc_final: 0.6859 (mmmm) REVERT: E 63 ARG cc_start: 0.7065 (ttp-170) cc_final: 0.6822 (tpt-90) REVERT: E 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6357 (mp10) REVERT: E 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6784 (mp0) REVERT: E 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6904 (mttm) REVERT: E 157 LYS cc_start: 0.7270 (mttm) cc_final: 0.6850 (mmmm) REVERT: e 63 ARG cc_start: 0.7065 (ttp-170) cc_final: 0.6792 (tpt-90) REVERT: e 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6352 (mp10) REVERT: e 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6787 (mp0) REVERT: e 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6906 (mttm) REVERT: e 157 LYS cc_start: 0.7261 (mttm) cc_final: 0.6859 (mmmm) REVERT: r 63 ARG cc_start: 0.7060 (ttp-170) cc_final: 0.6818 (tpt-90) REVERT: r 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6354 (mp10) REVERT: r 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6780 (mp0) REVERT: r 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6907 (mttm) REVERT: r 157 LYS cc_start: 0.7285 (mttm) cc_final: 0.6842 (mmmm) REVERT: G 63 ARG cc_start: 0.7057 (ttp-170) cc_final: 0.6785 (tpt-90) REVERT: G 86 GLN cc_start: 0.7238 (mm-40) cc_final: 0.6357 (mp10) REVERT: G 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6786 (mp0) REVERT: G 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6907 (mttm) REVERT: G 157 LYS cc_start: 0.7290 (mttm) cc_final: 0.6848 (mmmm) REVERT: I 63 ARG cc_start: 0.7066 (ttp-170) cc_final: 0.6822 (tpt-90) REVERT: I 86 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6356 (mp10) REVERT: I 140 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6797 (mp0) REVERT: I 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6907 (mttm) REVERT: I 157 LYS cc_start: 0.7281 (mttm) cc_final: 0.6848 (mmmm) REVERT: M 63 ARG cc_start: 0.7084 (ttp-170) cc_final: 0.6828 (tpt-90) REVERT: M 86 GLN cc_start: 0.7233 (mm-40) cc_final: 0.6391 (mp10) REVERT: M 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6786 (mp0) REVERT: M 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6903 (mttm) REVERT: M 157 LYS cc_start: 0.7264 (mttm) cc_final: 0.6843 (mmmm) REVERT: O 86 GLN cc_start: 0.7242 (mm-40) cc_final: 0.6358 (mp10) REVERT: O 140 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6778 (mp0) REVERT: O 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6907 (mttm) REVERT: O 157 LYS cc_start: 0.7274 (mttm) cc_final: 0.6858 (mmmm) REVERT: Q 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6390 (mp10) REVERT: Q 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6785 (mp0) REVERT: Q 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6908 (mttm) REVERT: Q 157 LYS cc_start: 0.7278 (mttm) cc_final: 0.6846 (mmmm) REVERT: S 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6391 (mp10) REVERT: S 140 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6783 (mp0) REVERT: S 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6909 (mttm) REVERT: S 157 LYS cc_start: 0.7260 (mttm) cc_final: 0.6857 (mmmm) REVERT: U 63 ARG cc_start: 0.7067 (ttp-170) cc_final: 0.6823 (tpt-90) REVERT: U 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6351 (mp10) REVERT: U 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6788 (mp0) REVERT: U 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6905 (mttm) REVERT: U 157 LYS cc_start: 0.7283 (mttm) cc_final: 0.6844 (mmmm) REVERT: W 86 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6389 (mp10) REVERT: W 140 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6783 (mp0) REVERT: W 143 LYS cc_start: 0.7295 (mtmt) cc_final: 0.6910 (mttm) REVERT: W 157 LYS cc_start: 0.7268 (mttm) cc_final: 0.6855 (mmmm) REVERT: Y 86 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6387 (mp10) REVERT: Y 140 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6776 (mp0) REVERT: Y 143 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6904 (mttm) REVERT: Y 157 LYS cc_start: 0.7266 (mttm) cc_final: 0.6860 (mmmm) REVERT: 2 86 GLN cc_start: 0.7231 (mm-40) cc_final: 0.6390 (mp10) REVERT: 2 140 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6786 (mp0) REVERT: 2 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6906 (mttm) REVERT: 2 157 LYS cc_start: 0.7281 (mttm) cc_final: 0.6840 (mmmm) REVERT: 4 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6391 (mp10) REVERT: 4 140 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6790 (mp0) REVERT: 4 143 LYS cc_start: 0.7290 (mtmt) cc_final: 0.6902 (mttm) REVERT: 4 157 LYS cc_start: 0.7274 (mttm) cc_final: 0.6859 (mmmm) REVERT: F 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6386 (mp10) REVERT: F 140 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6787 (mp0) REVERT: F 143 LYS cc_start: 0.7293 (mtmt) cc_final: 0.6905 (mttm) REVERT: F 157 LYS cc_start: 0.7263 (mttm) cc_final: 0.6860 (mmmm) REVERT: H 86 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6355 (mp10) REVERT: H 140 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6791 (mp0) REVERT: H 143 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6904 (mttm) REVERT: H 157 LYS cc_start: 0.7260 (mttm) cc_final: 0.6857 (mmmm) REVERT: P 86 GLN cc_start: 0.7234 (mm-40) cc_final: 0.6391 (mp10) REVERT: P 140 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6787 (mp0) REVERT: P 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6907 (mttm) REVERT: P 157 LYS cc_start: 0.7269 (mttm) cc_final: 0.6851 (mmmm) REVERT: X 86 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6388 (mp10) REVERT: X 140 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6789 (mp0) REVERT: X 143 LYS cc_start: 0.7298 (mtmt) cc_final: 0.6910 (mttm) REVERT: X 157 LYS cc_start: 0.7266 (mttm) cc_final: 0.6847 (mmmm) REVERT: 6 86 GLN cc_start: 0.7232 (mm-40) cc_final: 0.6355 (mp10) REVERT: 6 140 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6778 (mp0) REVERT: 6 143 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6907 (mttm) REVERT: 6 157 LYS cc_start: 0.7261 (mttm) cc_final: 0.6862 (mmmm) outliers start: 24 outliers final: 24 residues processed: 483 average time/residue: 1.6000 time to fit residues: 928.0506 Evaluate side-chains 480 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 456 time to evaluate : 3.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain K residue 117 LEU Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain r residue 117 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain M residue 117 LEU Chi-restraints excluded: chain O residue 117 LEU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain U residue 117 LEU Chi-restraints excluded: chain W residue 117 LEU Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain 2 residue 117 LEU Chi-restraints excluded: chain 4 residue 117 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain 6 residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 20.0000 chunk 298 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 324 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 332 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.182491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.171881 restraints weight = 2698675.581| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.60 r_work: 0.3316 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work: 0.3233 rms_B_bonded: 4.42 restraints_weight: 0.1250 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37800 Z= 0.226 Angle : 0.716 8.278 51264 Z= 0.390 Chirality : 0.039 0.155 5280 Planarity : 0.008 0.146 6936 Dihedral : 5.570 44.891 5208 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.02 % Allowed : 4.27 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.53 (0.11), residues: 4920 helix: 3.47 (0.07), residues: 4032 sheet: None (None), residues: 0 loop : 0.52 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP 2 93 HIS 0.004 0.001 HIS F 128 PHE 0.024 0.004 PHE U 41 TYR 0.022 0.003 TYR e 39 ARG 0.008 0.001 ARG G 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18405.11 seconds wall clock time: 315 minutes 44.04 seconds (18944.04 seconds total)