Starting phenix.real_space_refine on Sun Sep 29 14:56:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/09_2024/7a6b_11669.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/09_2024/7a6b_11669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/09_2024/7a6b_11669.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/09_2024/7a6b_11669.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/09_2024/7a6b_11669.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a6b_11669/09_2024/7a6b_11669.cif" } resolution = 1.33 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= 0.000 sd= 0.017 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 41494 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 23520 2.51 5 N 6672 2.21 5 O 11150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 456 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 41494 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1567 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: 1284 Chain: "1" Number of atoms: 1567 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: 1284 Chain: "K" Number of atoms: 1567 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: 1284 Chain: "a" Number of atoms: 1567 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: 1284 Chain: "B" Number of atoms: 1567 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: 1284 Chain: "E" Number of atoms: 1567 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: 1284 Chain: "e" Number of atoms: 1567 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: 1284 Chain: "r" Number of atoms: 1567 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: 1284 Chain: "G" Number of atoms: 1567 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: 1284 Chain: "I" Number of atoms: 1567 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: 1284 Chain: "M" Number of atoms: 1567 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: 1284 Chain: "O" Number of atoms: 1567 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: 1284 Chain: "Q" Number of atoms: 1567 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: 1284 Chain: "S" Number of atoms: 1567 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: 1284 Chain: "U" Number of atoms: 1567 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: 1284 Chain: "W" Number of atoms: 1567 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: 1284 Chain: "Y" Number of atoms: 1567 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: 1284 Chain: "2" Number of atoms: 1567 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: 1284 Chain: "4" Number of atoms: 1567 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: 1284 Chain: "F" Number of atoms: 1567 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: 1284 Chain: "H" Number of atoms: 1567 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: 1284 Chain: "P" Number of atoms: 1567 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: 1284 Chain: "X" Number of atoms: 1567 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: 1284 Chain: "6" Number of atoms: 1567 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: 1284 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: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "1" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "K" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "a" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "E" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "e" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "r" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "G" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "I" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "M" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "O" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 162 Classifications: {'water': 162} Link IDs: {None: 161} Chain: "Q" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "S" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "U" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "W" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "Y" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "2" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "4" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "F" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "H" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "P" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "X" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Chain: "6" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 160 Classifications: {'water': 160} Link IDs: {None: 159} Residues with excluded nonbonded symmetry interactions: 432 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 ALYS A 87 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 87 " 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 ASER A 113 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 113 " occ=0.50 residue: pdb=" N AILE A 133 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 133 " occ=0.50 ... (remaining 420 not shown) Time building chain proxies: 28.58, per 1000 atoms: 0.69 Number of scatterers: 41494 At special positions: 0 Unit cell: (131.364, 131.364, 131.364, 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 11150 8.00 N 6672 7.00 C 23520 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: 8.38 Conformation dependent library (CDL) restraints added in 6.1 seconds 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8784 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: 2.33 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: 3.619A pdb=" N GLU A 167 " --> pdb=" O ASER 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: 3.620A pdb=" N GLU 1 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU K 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU a 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU B 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU E 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU e 167 " --> pdb=" O ASER 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: 3.618A pdb=" N GLU r 167 " --> pdb=" O ASER 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: 3.618A pdb=" N GLU G 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU I 167 " --> pdb=" O ASER 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: 3.620A pdb=" N GLU M 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU O 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU Q 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU S 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU U 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU W 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU Y 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU 2 167 " --> pdb=" O ASER 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: 3.620A pdb=" N GLU 4 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU F 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU H 167 " --> pdb=" O ASER 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: 3.621A pdb=" N GLU P 167 " --> pdb=" O ASER 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: 3.619A pdb=" N GLU X 167 " --> pdb=" O ASER 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: 3.620A pdb=" N GLU 6 167 " --> pdb=" O ASER 6 163 " (cutoff:3.500A) 3096 hydrogen bonds defined for protein. 9552 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: 12.39 Time building geometry restraints manager: 9.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8432 1.32 - 1.45: 8657 1.45 - 1.58: 21335 1.58 - 1.71: 0 1.71 - 1.84: 216 Bond restraints: 38640 Sorted by residual: bond pdb=" C BSER a 163 " pdb=" O BSER a 163 " ideal model delta sigma weight residual 1.236 1.357 -0.122 1.32e-02 5.74e+03 8.50e+01 bond pdb=" C BSER K 163 " pdb=" O BSER K 163 " ideal model delta sigma weight residual 1.236 1.353 -0.117 1.32e-02 5.74e+03 7.83e+01 bond pdb=" C BSER A 163 " pdb=" O BSER A 163 " ideal model delta sigma weight residual 1.236 1.330 -0.094 1.32e-02 5.74e+03 5.09e+01 bond pdb=" C BSER 1 163 " pdb=" O BSER 1 163 " ideal model delta sigma weight residual 1.236 1.319 -0.083 1.32e-02 5.74e+03 3.96e+01 bond pdb=" C BSER B 163 " pdb=" O BSER B 163 " ideal model delta sigma weight residual 1.236 1.309 -0.074 1.32e-02 5.74e+03 3.11e+01 ... (remaining 38635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 41032 1.82 - 3.63: 9836 3.63 - 5.45: 1159 5.45 - 7.26: 407 7.26 - 9.08: 30 Bond angle restraints: 52464 Sorted by residual: angle pdb=" CA ASP W 150 " pdb=" CB ASP W 150 " pdb=" CG ASP W 150 " ideal model delta sigma weight residual 112.60 119.07 -6.47 1.00e+00 1.00e+00 4.19e+01 angle pdb=" CA ASP K 150 " pdb=" CB ASP K 150 " pdb=" CG ASP K 150 " ideal model delta sigma weight residual 112.60 119.05 -6.45 1.00e+00 1.00e+00 4.16e+01 angle pdb=" CA ASP 1 150 " pdb=" CB ASP 1 150 " pdb=" CG ASP 1 150 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" CA ASP O 150 " pdb=" CB ASP O 150 " pdb=" CG ASP O 150 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 angle pdb=" CA ASP Q 150 " pdb=" CB ASP Q 150 " pdb=" CG ASP Q 150 " ideal model delta sigma weight residual 112.60 119.04 -6.44 1.00e+00 1.00e+00 4.14e+01 ... (remaining 52459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 22945 34.98 - 69.96: 719 69.96 - 104.93: 72 104.93 - 139.91: 0 139.91 - 174.89: 24 Dihedral angle restraints: 23760 sinusoidal: 9864 harmonic: 13896 Sorted by residual: dihedral pdb=" CB BGLU A 162 " pdb=" CG BGLU A 162 " pdb=" CD BGLU A 162 " pdb=" OE1BGLU A 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.89 -174.89 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB BGLU 1 162 " pdb=" CG BGLU 1 162 " pdb=" CD BGLU 1 162 " pdb=" OE1BGLU 1 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.68 -174.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB BGLU K 162 " pdb=" CG BGLU K 162 " pdb=" CD BGLU K 162 " pdb=" OE1BGLU K 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.49 -174.49 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 23757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2981 0.087 - 0.175: 1560 0.175 - 0.262: 685 0.262 - 0.350: 126 0.350 - 0.437: 48 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CA TYR P 39 " pdb=" N TYR P 39 " pdb=" C TYR P 39 " pdb=" CB TYR P 39 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA TYR 2 39 " pdb=" N TYR 2 39 " pdb=" C TYR 2 39 " pdb=" CB TYR 2 39 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 5397 not shown) Planarity restraints: 7128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 137 " 0.103 2.00e-02 2.50e+03 6.06e-02 7.35e+01 pdb=" CG TYR K 137 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR K 137 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR K 137 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR K 137 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR K 137 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR K 137 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR K 137 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 137 " -0.103 2.00e-02 2.50e+03 6.06e-02 7.35e+01 pdb=" CG TYR a 137 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR a 137 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR a 137 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR a 137 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR a 137 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR a 137 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR a 137 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 137 " -0.103 2.00e-02 2.50e+03 6.06e-02 7.35e+01 pdb=" CG TYR B 137 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 137 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TYR B 137 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 137 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 137 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR B 137 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR B 137 " -0.086 2.00e-02 2.50e+03 ... (remaining 7125 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 221 2.49 - 3.10: 35763 3.10 - 3.70: 77296 3.70 - 4.30: 125189 4.30 - 4.90: 187010 Nonbonded interactions: 425479 Sorted by model distance: nonbonded pdb=" OE2 GLU K 101 " pdb=" NH2BARG K 156 " model vdw 1.893 3.120 nonbonded pdb=" OE2 GLU G 101 " pdb=" NH2BARG G 156 " model vdw 1.893 3.120 nonbonded pdb=" OE2 GLU 1 101 " pdb=" NH2BARG 1 156 " model vdw 1.893 3.120 nonbonded pdb=" OE2 GLU U 101 " pdb=" NH2BARG U 156 " model vdw 1.893 3.120 nonbonded pdb=" OE2 GLU O 101 " pdb=" NH2BARG O 156 " model vdw 1.893 3.120 ... (remaining 425474 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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 86 or resid 88 through 93 or resid 95 through 108 or resid 110 through \ 112 or resid 114 through 132 or resid 134 through 155 or resid 157 through 161 \ or resid 166 through 171 or resid 173 through 176 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=0.91 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: 5.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.410 Construct map_model_manager: 0.040 Extract box with map and model: 1.550 Check model and map are aligned: 0.210 Set scattering table: 0.300 Process input model: 86.320 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 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 0.122 38640 Z= 0.967 Angle : 1.602 9.077 52464 Z= 1.097 Chirality : 0.123 0.437 5400 Planarity : 0.011 0.061 7128 Dihedral : 16.776 174.891 14976 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.17 % Allowed : 3.35 % Favored : 92.49 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.11), residues: 5136 helix: 1.91 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.84 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.011 TRP 1 93 HIS 0.025 0.008 HIS H 173 PHE 0.041 0.011 PHE I 41 TYR 0.103 0.025 TYR r 137 ARG 0.015 0.005 ARG 6 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 744 time to evaluate : 3.378 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: A 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.6095 (m-30) REVERT: A 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6337 (tppt) REVERT: 1 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.6103 (m-30) REVERT: 1 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: K 89 ASP cc_start: 0.6376 (m-30) cc_final: 0.6101 (m-30) REVERT: K 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6340 (tppt) REVERT: a 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.6100 (m-30) REVERT: a 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6339 (tppt) REVERT: B 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6089 (m-30) REVERT: B 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6342 (tppt) REVERT: E 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6088 (m-30) REVERT: E 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: e 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.6096 (m-30) REVERT: e 119 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6340 (tppt) REVERT: r 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.6100 (m-30) REVERT: r 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6339 (tppt) REVERT: G 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.6103 (m-30) REVERT: G 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6341 (tppt) REVERT: I 89 ASP cc_start: 0.6372 (m-30) cc_final: 0.6095 (m-30) REVERT: I 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: M 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6091 (m-30) REVERT: M 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6338 (tppt) REVERT: O 89 ASP cc_start: 0.6376 (m-30) cc_final: 0.6102 (m-30) REVERT: O 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: Q 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.6103 (m-30) REVERT: Q 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6342 (tppt) REVERT: S 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6091 (m-30) REVERT: S 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: U 89 ASP cc_start: 0.6363 (m-30) cc_final: 0.6086 (m-30) REVERT: U 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: W 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.6091 (m-30) REVERT: W 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: Y 89 ASP cc_start: 0.6377 (m-30) cc_final: 0.6102 (m-30) REVERT: Y 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6339 (tppt) REVERT: 2 89 ASP cc_start: 0.6363 (m-30) cc_final: 0.6086 (m-30) REVERT: 2 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6337 (tppt) REVERT: 4 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.6093 (m-30) REVERT: 4 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6341 (tppt) REVERT: F 89 ASP cc_start: 0.6365 (m-30) cc_final: 0.6088 (m-30) REVERT: F 119 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6339 (tppt) REVERT: H 89 ASP cc_start: 0.6359 (m-30) cc_final: 0.6080 (m-30) REVERT: H 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6340 (tppt) REVERT: P 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.6095 (m-30) REVERT: P 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6339 (tppt) REVERT: X 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.6094 (m-30) REVERT: X 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6343 (tppt) REVERT: 6 89 ASP cc_start: 0.6365 (m-30) cc_final: 0.6090 (m-30) REVERT: 6 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6338 (tppt) outliers start: 72 outliers final: 0 residues processed: 768 average time/residue: 1.3519 time to fit residues: 1258.6138 Evaluate side-chains 546 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 546 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 105 optimal weight: 20.0000 chunk 208 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN A 86 GLN A 98 ASN 1 60 HIS 1 83 GLN 1 86 GLN 1 98 ASN 1 136 HIS K 60 HIS K 83 GLN K 86 GLN K 98 ASN K 136 HIS a 60 HIS a 83 GLN a 86 GLN a 98 ASN a 136 HIS B 60 HIS B 83 GLN B 86 GLN B 98 ASN E 60 HIS E 83 GLN E 86 GLN E 98 ASN e 60 HIS e 83 GLN e 86 GLN e 98 ASN r 60 HIS r 83 GLN r 86 GLN r 98 ASN r 136 HIS G 60 HIS G 83 GLN G 86 GLN G 98 ASN G 136 HIS I 60 HIS I 83 GLN I 86 GLN I 98 ASN I 136 HIS M 60 HIS M 83 GLN M 86 GLN M 98 ASN M 136 HIS O 60 HIS O 83 GLN O 86 GLN O 98 ASN O 136 HIS Q 60 HIS Q 83 GLN Q 86 GLN Q 98 ASN Q 136 HIS S 60 HIS S 83 GLN S 86 GLN S 98 ASN S 136 HIS U 60 HIS U 83 GLN U 86 GLN U 98 ASN U 136 HIS W 60 HIS W 83 GLN W 86 GLN W 98 ASN W 136 HIS Y 60 HIS Y 83 GLN Y 86 GLN Y 98 ASN Y 136 HIS 2 60 HIS 2 83 GLN 2 86 GLN 2 98 ASN 2 136 HIS 4 60 HIS 4 83 GLN 4 86 GLN 4 98 ASN 4 136 HIS F 60 HIS F 83 GLN F 86 GLN F 98 ASN H 60 HIS H 83 GLN H 86 GLN H 98 ASN P 60 HIS P 83 GLN P 86 GLN P 98 ASN P 136 HIS X 60 HIS X 83 GLN X 86 GLN X 98 ASN X 136 HIS 6 60 HIS 6 83 GLN 6 86 GLN 6 98 ASN 6 136 HIS Total number of N/Q/H flips: 114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 38640 Z= 0.173 Angle : 0.610 5.586 52464 Z= 0.338 Chirality : 0.038 0.158 5400 Planarity : 0.004 0.043 7128 Dihedral : 4.665 18.607 5328 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.38 % Allowed : 3.47 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.11), residues: 5136 helix: 3.34 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.74 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP Q 93 HIS 0.013 0.002 HIS K 60 PHE 0.021 0.002 PHE a 41 TYR 0.022 0.003 TYR F 39 ARG 0.007 0.001 ARG 1 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 3.248 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 89 ASP cc_start: 0.6354 (m-30) cc_final: 0.5967 (m-30) REVERT: A 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6345 (tppt) REVERT: 1 89 ASP cc_start: 0.6353 (m-30) cc_final: 0.5964 (m-30) REVERT: 1 119 LYS cc_start: 0.6835 (ttmm) cc_final: 0.6342 (tppt) REVERT: K 89 ASP cc_start: 0.6351 (m-30) cc_final: 0.5962 (m-30) REVERT: K 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6345 (tppt) REVERT: a 89 ASP cc_start: 0.6353 (m-30) cc_final: 0.5964 (m-30) REVERT: a 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6343 (tppt) REVERT: B 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5958 (m-30) REVERT: B 119 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6345 (tppt) REVERT: E 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5958 (m-30) REVERT: E 119 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6345 (tppt) REVERT: e 89 ASP cc_start: 0.6351 (m-30) cc_final: 0.5965 (m-30) REVERT: e 119 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6345 (tppt) REVERT: r 89 ASP cc_start: 0.6352 (m-30) cc_final: 0.5964 (m-30) REVERT: r 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6344 (tppt) REVERT: G 89 ASP cc_start: 0.6351 (m-30) cc_final: 0.5962 (m-30) REVERT: G 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6345 (tppt) REVERT: I 89 ASP cc_start: 0.6349 (m-30) cc_final: 0.5964 (m-30) REVERT: I 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6346 (tppt) REVERT: M 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5958 (m-30) REVERT: M 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6345 (tppt) REVERT: O 89 ASP cc_start: 0.6353 (m-30) cc_final: 0.5965 (m-30) REVERT: O 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6345 (tppt) REVERT: Q 89 ASP cc_start: 0.6350 (m-30) cc_final: 0.5961 (m-30) REVERT: Q 119 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6347 (tppt) REVERT: S 89 ASP cc_start: 0.6344 (m-30) cc_final: 0.5957 (m-30) REVERT: S 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6344 (tppt) REVERT: U 89 ASP cc_start: 0.6346 (m-30) cc_final: 0.5961 (m-30) REVERT: U 119 LYS cc_start: 0.6839 (ttmm) cc_final: 0.6346 (tppt) REVERT: W 89 ASP cc_start: 0.6344 (m-30) cc_final: 0.5958 (m-30) REVERT: W 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6344 (tppt) REVERT: Y 89 ASP cc_start: 0.6352 (m-30) cc_final: 0.5964 (m-30) REVERT: Y 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6345 (tppt) REVERT: 2 89 ASP cc_start: 0.6348 (m-30) cc_final: 0.5963 (m-30) REVERT: 2 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6346 (tppt) REVERT: 4 89 ASP cc_start: 0.6351 (m-30) cc_final: 0.5963 (m-30) REVERT: 4 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6345 (tppt) REVERT: F 89 ASP cc_start: 0.6351 (m-30) cc_final: 0.5965 (m-30) REVERT: F 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6345 (tppt) REVERT: H 89 ASP cc_start: 0.6345 (m-30) cc_final: 0.5957 (m-30) REVERT: H 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6345 (tppt) REVERT: P 89 ASP cc_start: 0.6352 (m-30) cc_final: 0.5966 (m-30) REVERT: P 119 LYS cc_start: 0.6836 (ttmm) cc_final: 0.6343 (tppt) REVERT: X 89 ASP cc_start: 0.6352 (m-30) cc_final: 0.5965 (m-30) REVERT: X 119 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6344 (tppt) REVERT: 6 89 ASP cc_start: 0.6351 (m-30) cc_final: 0.5964 (m-30) REVERT: 6 119 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6344 (tppt) outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 1.4211 time to fit residues: 1148.3880 Evaluate side-chains 536 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 308 optimal weight: 0.9990 chunk 252 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 371 optimal weight: 10.0000 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 chunk 368 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B A 86 GLN 1 75 GLN B 1 86 GLN K 75 GLN B K 86 GLN a 75 GLN B a 86 GLN B 75 GLN B B 86 GLN E 75 GLN B E 86 GLN e 75 GLN B e 86 GLN r 75 GLN B r 86 GLN G 75 GLN B G 86 GLN I 75 GLN B I 86 GLN M 75 GLN B M 86 GLN O 75 GLN B O 86 GLN Q 75 GLN B Q 86 GLN S 75 GLN B S 86 GLN U 75 GLN B U 86 GLN W 75 GLN B W 86 GLN Y 75 GLN B Y 86 GLN 2 75 GLN B 2 86 GLN 4 75 GLN B 4 86 GLN F 75 GLN B F 86 GLN H 75 GLN B H 86 GLN P 75 GLN B P 86 GLN X 75 GLN B X 86 GLN 6 75 GLN B 6 86 GLN 6 136 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 38640 Z= 0.201 Angle : 0.654 6.150 52464 Z= 0.363 Chirality : 0.039 0.152 5400 Planarity : 0.004 0.052 7128 Dihedral : 4.837 22.399 5328 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.38 % Allowed : 2.38 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.39 (0.11), residues: 5136 helix: 3.35 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.74 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP Q 93 HIS 0.007 0.002 HIS A 60 PHE 0.024 0.003 PHE G 41 TYR 0.021 0.003 TYR 6 39 ARG 0.011 0.001 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.6371 (m-30) cc_final: 0.5980 (m-30) REVERT: A 119 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6393 (tppt) REVERT: 1 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5980 (m-30) REVERT: 1 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6391 (tppt) REVERT: K 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5980 (m-30) REVERT: K 119 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6391 (tppt) REVERT: a 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5981 (m-30) REVERT: a 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6394 (tppt) REVERT: B 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5975 (m-30) REVERT: B 119 LYS cc_start: 0.6891 (ttmm) cc_final: 0.6395 (tppt) REVERT: E 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5975 (m-30) REVERT: E 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6393 (tppt) REVERT: e 89 ASP cc_start: 0.6371 (m-30) cc_final: 0.5981 (m-30) REVERT: e 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6393 (tppt) REVERT: r 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5981 (m-30) REVERT: r 119 LYS cc_start: 0.6892 (ttmm) cc_final: 0.6397 (tppt) REVERT: G 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5980 (m-30) REVERT: G 119 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6394 (tppt) REVERT: I 89 ASP cc_start: 0.6370 (m-30) cc_final: 0.5980 (m-30) REVERT: I 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6394 (tppt) REVERT: M 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5973 (m-30) REVERT: M 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6393 (tppt) REVERT: O 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5981 (m-30) REVERT: O 119 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6392 (tppt) REVERT: Q 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5980 (m-30) REVERT: Q 119 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6394 (tppt) REVERT: S 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5974 (m-30) REVERT: S 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6393 (tppt) REVERT: U 89 ASP cc_start: 0.6370 (m-30) cc_final: 0.5980 (m-30) REVERT: U 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6394 (tppt) REVERT: W 89 ASP cc_start: 0.6365 (m-30) cc_final: 0.5973 (m-30) REVERT: W 119 LYS cc_start: 0.6886 (ttmm) cc_final: 0.6391 (tppt) REVERT: Y 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5981 (m-30) REVERT: Y 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6391 (tppt) REVERT: 2 89 ASP cc_start: 0.6370 (m-30) cc_final: 0.5980 (m-30) REVERT: 2 119 LYS cc_start: 0.6889 (ttmm) cc_final: 0.6394 (tppt) REVERT: 4 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5980 (m-30) REVERT: 4 119 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6394 (tppt) REVERT: F 89 ASP cc_start: 0.6372 (m-30) cc_final: 0.5982 (m-30) REVERT: F 119 LYS cc_start: 0.6890 (ttmm) cc_final: 0.6393 (tppt) REVERT: H 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5976 (m-30) REVERT: H 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6393 (tppt) REVERT: P 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5982 (m-30) REVERT: P 119 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6392 (tppt) REVERT: X 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.5983 (m-30) REVERT: X 119 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6392 (tppt) REVERT: 6 89 ASP cc_start: 0.6372 (m-30) cc_final: 0.5982 (m-30) REVERT: 6 119 LYS cc_start: 0.6888 (ttmm) cc_final: 0.6394 (tppt) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 1.5503 time to fit residues: 997.5712 Evaluate side-chains 528 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 3.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 192 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 chunk 249 optimal weight: 20.0000 chunk 372 optimal weight: 0.5980 chunk 394 optimal weight: 8.9990 chunk 194 optimal weight: 0.6980 chunk 353 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 86 GLN K 86 GLN a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 86 GLN G 86 GLN I 86 GLN M 86 GLN O 86 GLN Q 86 GLN S 86 GLN U 60 HIS U 86 GLN W 86 GLN Y 86 GLN 2 86 GLN 4 86 GLN F 86 GLN H 86 GLN P 86 GLN X 86 GLN 6 86 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 38640 Z= 0.139 Angle : 0.543 5.120 52464 Z= 0.301 Chirality : 0.035 0.143 5400 Planarity : 0.004 0.059 7128 Dihedral : 4.489 18.712 5328 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.38 % Allowed : 2.38 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.04 (0.11), residues: 5136 helix: 3.81 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.85 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP U 93 HIS 0.006 0.001 HIS G 60 PHE 0.016 0.002 PHE r 41 TYR 0.018 0.002 TYR G 39 ARG 0.006 0.001 ARG a 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 3.253 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 89 ASP cc_start: 0.6342 (m-30) cc_final: 0.5959 (m-30) REVERT: A 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6310 (tppt) REVERT: 1 89 ASP cc_start: 0.6343 (m-30) cc_final: 0.5959 (m-30) REVERT: 1 119 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6307 (tppt) REVERT: K 89 ASP cc_start: 0.6336 (m-30) cc_final: 0.5937 (m-30) REVERT: K 119 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6309 (tppt) REVERT: a 89 ASP cc_start: 0.6337 (m-30) cc_final: 0.5938 (m-30) REVERT: a 119 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6308 (tppt) REVERT: B 89 ASP cc_start: 0.6329 (m-30) cc_final: 0.5931 (m-30) REVERT: B 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6310 (tppt) REVERT: E 89 ASP cc_start: 0.6336 (m-30) cc_final: 0.5953 (m-30) REVERT: E 119 LYS cc_start: 0.6803 (ttmm) cc_final: 0.6310 (tppt) REVERT: e 89 ASP cc_start: 0.6335 (m-30) cc_final: 0.5940 (m-30) REVERT: e 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6310 (tppt) REVERT: r 89 ASP cc_start: 0.6337 (m-30) cc_final: 0.5938 (m-30) REVERT: r 119 LYS cc_start: 0.6799 (ttmm) cc_final: 0.6307 (tppt) REVERT: G 89 ASP cc_start: 0.6336 (m-30) cc_final: 0.5938 (m-30) REVERT: G 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6310 (tppt) REVERT: I 89 ASP cc_start: 0.6333 (m-30) cc_final: 0.5938 (m-30) REVERT: I 119 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6309 (tppt) REVERT: M 89 ASP cc_start: 0.6329 (m-30) cc_final: 0.5931 (m-30) REVERT: M 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6310 (tppt) REVERT: O 89 ASP cc_start: 0.6336 (m-30) cc_final: 0.5938 (m-30) REVERT: O 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6310 (tppt) REVERT: Q 89 ASP cc_start: 0.6336 (m-30) cc_final: 0.5937 (m-30) REVERT: Q 119 LYS cc_start: 0.6803 (ttmm) cc_final: 0.6311 (tppt) REVERT: S 89 ASP cc_start: 0.6328 (m-30) cc_final: 0.5932 (m-30) REVERT: S 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6310 (tppt) REVERT: U 89 ASP cc_start: 0.6334 (m-30) cc_final: 0.5931 (m-30) REVERT: U 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6310 (tppt) REVERT: W 89 ASP cc_start: 0.6326 (m-30) cc_final: 0.5929 (m-30) REVERT: W 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6310 (tppt) REVERT: Y 89 ASP cc_start: 0.6336 (m-30) cc_final: 0.5938 (m-30) REVERT: Y 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6310 (tppt) REVERT: 2 89 ASP cc_start: 0.6333 (m-30) cc_final: 0.5938 (m-30) REVERT: 2 119 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6308 (tppt) REVERT: 4 89 ASP cc_start: 0.6337 (m-30) cc_final: 0.5939 (m-30) REVERT: 4 119 LYS cc_start: 0.6803 (ttmm) cc_final: 0.6311 (tppt) REVERT: F 89 ASP cc_start: 0.6334 (m-30) cc_final: 0.5940 (m-30) REVERT: F 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6310 (tppt) REVERT: H 89 ASP cc_start: 0.6330 (m-30) cc_final: 0.5933 (m-30) REVERT: H 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6309 (tppt) REVERT: P 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5941 (m-30) REVERT: P 119 LYS cc_start: 0.6802 (ttmm) cc_final: 0.6309 (tppt) REVERT: X 89 ASP cc_start: 0.6336 (m-30) cc_final: 0.5939 (m-30) REVERT: X 119 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6309 (tppt) REVERT: 6 89 ASP cc_start: 0.6338 (m-30) cc_final: 0.5941 (m-30) REVERT: 6 119 LYS cc_start: 0.6800 (ttmm) cc_final: 0.6308 (tppt) outliers start: 0 outliers final: 0 residues processed: 550 average time/residue: 1.4566 time to fit residues: 959.4390 Evaluate side-chains 504 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 293 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 272 optimal weight: 0.0770 chunk 0 optimal weight: 30.0000 chunk 201 optimal weight: 10.0000 chunk 353 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 139 ASN 1 86 GLN 1 139 ASN K 86 GLN K 139 ASN a 86 GLN a 139 ASN B 86 GLN B 139 ASN E 86 GLN E 139 ASN e 86 GLN e 139 ASN r 86 GLN r 139 ASN G 86 GLN G 139 ASN I 86 GLN I 139 ASN M 86 GLN M 139 ASN O 86 GLN O 139 ASN Q 86 GLN Q 139 ASN S 86 GLN S 139 ASN U 60 HIS U 86 GLN U 139 ASN W 86 GLN W 139 ASN Y 86 GLN Y 139 ASN 2 86 GLN 2 139 ASN 4 60 HIS 4 86 GLN 4 139 ASN F 86 GLN F 139 ASN H 86 GLN H 139 ASN P 86 GLN P 139 ASN X 86 GLN X 139 ASN 6 86 GLN 6 139 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 38640 Z= 0.231 Angle : 0.689 6.324 52464 Z= 0.382 Chirality : 0.040 0.145 5400 Planarity : 0.004 0.043 7128 Dihedral : 4.879 25.530 5328 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 2.98 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.34 (0.11), residues: 5136 helix: 3.32 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.66 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP 4 93 HIS 0.005 0.001 HIS A 128 PHE 0.027 0.004 PHE K 41 TYR 0.023 0.003 TYR P 39 ARG 0.008 0.001 ARG U 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 3.217 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 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5976 (m-30) REVERT: A 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6390 (tppt) REVERT: 1 89 ASP cc_start: 0.6385 (m-30) cc_final: 0.5976 (m-30) REVERT: 1 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6389 (tppt) REVERT: K 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5974 (m-30) REVERT: K 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6389 (tppt) REVERT: a 89 ASP cc_start: 0.6384 (m-30) cc_final: 0.5976 (m-30) REVERT: a 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6388 (tppt) REVERT: B 89 ASP cc_start: 0.6379 (m-30) cc_final: 0.5989 (m-30) REVERT: B 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6390 (tppt) REVERT: E 89 ASP cc_start: 0.6377 (m-30) cc_final: 0.5970 (m-30) REVERT: E 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6390 (tppt) REVERT: e 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5977 (m-30) REVERT: e 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6390 (tppt) REVERT: r 89 ASP cc_start: 0.6384 (m-30) cc_final: 0.5976 (m-30) REVERT: r 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6388 (tppt) REVERT: G 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5991 (m-30) REVERT: G 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6388 (tppt) REVERT: I 89 ASP cc_start: 0.6379 (m-30) cc_final: 0.5974 (m-30) REVERT: I 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6390 (tppt) REVERT: M 89 ASP cc_start: 0.6377 (m-30) cc_final: 0.5969 (m-30) REVERT: M 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6389 (tppt) REVERT: O 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5975 (m-30) REVERT: O 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6389 (tppt) REVERT: Q 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5973 (m-30) REVERT: Q 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6388 (tppt) REVERT: S 89 ASP cc_start: 0.6378 (m-30) cc_final: 0.5988 (m-30) REVERT: S 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6389 (tppt) REVERT: U 89 ASP cc_start: 0.6378 (m-30) cc_final: 0.5991 (m-30) REVERT: U 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6389 (tppt) REVERT: W 89 ASP cc_start: 0.6375 (m-30) cc_final: 0.5967 (m-30) REVERT: W 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6389 (tppt) REVERT: Y 89 ASP cc_start: 0.6382 (m-30) cc_final: 0.5991 (m-30) REVERT: Y 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6389 (tppt) REVERT: 2 89 ASP cc_start: 0.6378 (m-30) cc_final: 0.5990 (m-30) REVERT: 2 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6389 (tppt) REVERT: 4 89 ASP cc_start: 0.6381 (m-30) cc_final: 0.5990 (m-30) REVERT: 4 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6388 (tppt) REVERT: F 89 ASP cc_start: 0.6384 (m-30) cc_final: 0.5996 (m-30) REVERT: F 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6390 (tppt) REVERT: H 89 ASP cc_start: 0.6378 (m-30) cc_final: 0.5989 (m-30) REVERT: H 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6390 (tppt) REVERT: P 89 ASP cc_start: 0.6386 (m-30) cc_final: 0.5996 (m-30) REVERT: P 119 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6389 (tppt) REVERT: X 89 ASP cc_start: 0.6386 (m-30) cc_final: 0.5995 (m-30) REVERT: X 119 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6389 (tppt) REVERT: 6 89 ASP cc_start: 0.6384 (m-30) cc_final: 0.5994 (m-30) REVERT: 6 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6388 (tppt) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 1.5073 time to fit residues: 931.3325 Evaluate side-chains 519 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 77 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 10.0000 chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 32 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 86 GLN K 86 GLN a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 86 GLN G 86 GLN I 86 GLN M 86 GLN O 86 GLN Q 86 GLN S 86 GLN U 60 HIS U 86 GLN W 86 GLN Y 86 GLN 2 86 GLN 4 60 HIS 4 86 GLN F 86 GLN H 86 GLN P 86 GLN X 86 GLN 6 86 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 38640 Z= 0.263 Angle : 0.734 7.863 52464 Z= 0.407 Chirality : 0.041 0.150 5400 Planarity : 0.005 0.051 7128 Dihedral : 4.936 25.571 5328 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 2.98 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.11), residues: 5136 helix: 3.07 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.48 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP P 93 HIS 0.005 0.002 HIS 4 57 PHE 0.028 0.004 PHE U 41 TYR 0.024 0.004 TYR W 39 ARG 0.010 0.001 ARG U 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 3.258 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 89 ASP cc_start: 0.6371 (m-30) cc_final: 0.5964 (m-30) REVERT: A 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6387 (tppt) REVERT: 1 89 ASP cc_start: 0.6372 (m-30) cc_final: 0.5962 (m-30) REVERT: 1 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6386 (tppt) REVERT: K 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5965 (m-30) REVERT: K 119 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6385 (tppt) REVERT: a 89 ASP cc_start: 0.6371 (m-30) cc_final: 0.5961 (m-30) REVERT: a 119 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6385 (tppt) REVERT: B 89 ASP cc_start: 0.6364 (m-30) cc_final: 0.5956 (m-30) REVERT: B 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6386 (tppt) REVERT: E 89 ASP cc_start: 0.6364 (m-30) cc_final: 0.5956 (m-30) REVERT: E 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6386 (tppt) REVERT: e 89 ASP cc_start: 0.6369 (m-30) cc_final: 0.5963 (m-30) REVERT: e 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6387 (tppt) REVERT: r 89 ASP cc_start: 0.6371 (m-30) cc_final: 0.5962 (m-30) REVERT: r 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6386 (tppt) REVERT: G 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5982 (m-30) REVERT: G 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6385 (tppt) REVERT: I 89 ASP cc_start: 0.6368 (m-30) cc_final: 0.5961 (m-30) REVERT: I 119 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6385 (tppt) REVERT: M 89 ASP cc_start: 0.6363 (m-30) cc_final: 0.5955 (m-30) REVERT: M 119 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6384 (tppt) REVERT: O 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5965 (m-30) REVERT: O 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6385 (tppt) REVERT: Q 89 ASP cc_start: 0.6371 (m-30) cc_final: 0.5962 (m-30) REVERT: Q 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6386 (tppt) REVERT: S 89 ASP cc_start: 0.6363 (m-30) cc_final: 0.5954 (m-30) REVERT: S 119 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6386 (tppt) REVERT: U 89 ASP cc_start: 0.6367 (m-30) cc_final: 0.5961 (m-30) REVERT: U 119 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6384 (tppt) REVERT: W 89 ASP cc_start: 0.6363 (m-30) cc_final: 0.5955 (m-30) REVERT: W 119 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6385 (tppt) REVERT: Y 89 ASP cc_start: 0.6370 (m-30) cc_final: 0.5961 (m-30) REVERT: Y 119 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6384 (tppt) REVERT: 2 89 ASP cc_start: 0.6367 (m-30) cc_final: 0.5961 (m-30) REVERT: 2 119 LYS cc_start: 0.6877 (ttmm) cc_final: 0.6385 (tppt) REVERT: 4 89 ASP cc_start: 0.6370 (m-30) cc_final: 0.5962 (m-30) REVERT: 4 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6386 (tppt) REVERT: F 89 ASP cc_start: 0.6370 (m-30) cc_final: 0.5981 (m-30) REVERT: F 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6386 (tppt) REVERT: H 89 ASP cc_start: 0.6365 (m-30) cc_final: 0.5958 (m-30) REVERT: H 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6387 (tppt) REVERT: P 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5981 (m-30) REVERT: P 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6386 (tppt) REVERT: X 89 ASP cc_start: 0.6372 (m-30) cc_final: 0.5964 (m-30) REVERT: X 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6386 (tppt) REVERT: 6 89 ASP cc_start: 0.6370 (m-30) cc_final: 0.5979 (m-30) REVERT: 6 119 LYS cc_start: 0.6878 (ttmm) cc_final: 0.6386 (tppt) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 1.5117 time to fit residues: 925.6589 Evaluate side-chains 508 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 508 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 0.8980 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 40.0000 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 86 GLN K 86 GLN a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 86 GLN G 86 GLN I 86 GLN M 86 GLN O 86 GLN Q 86 GLN S 86 GLN U 60 HIS U 86 GLN W 86 GLN Y 86 GLN 2 86 GLN 4 60 HIS 4 86 GLN F 86 GLN H 86 GLN P 86 GLN X 86 GLN 6 86 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 38640 Z= 0.172 Angle : 0.622 8.851 52464 Z= 0.343 Chirality : 0.037 0.151 5400 Planarity : 0.004 0.036 7128 Dihedral : 4.684 19.422 5328 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 2.98 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.59 (0.11), residues: 5136 helix: 3.52 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.63 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP X 93 HIS 0.007 0.001 HIS 1 60 PHE 0.020 0.003 PHE M 41 TYR 0.019 0.002 TYR F 39 ARG 0.009 0.001 ARG M 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 3.270 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 89 ASP cc_start: 0.6371 (m-30) cc_final: 0.5983 (m-30) REVERT: A 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6345 (tppt) REVERT: 1 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5983 (m-30) REVERT: 1 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6344 (tppt) REVERT: K 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5967 (m-30) REVERT: K 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6346 (tppt) REVERT: a 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5983 (m-30) REVERT: a 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6344 (tppt) REVERT: B 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5962 (m-30) REVERT: B 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6346 (tppt) REVERT: E 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5977 (m-30) REVERT: E 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6346 (tppt) REVERT: e 89 ASP cc_start: 0.6371 (m-30) cc_final: 0.5984 (m-30) REVERT: e 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6345 (tppt) REVERT: r 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5968 (m-30) REVERT: r 119 LYS cc_start: 0.6840 (ttmm) cc_final: 0.6344 (tppt) REVERT: G 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5968 (m-30) REVERT: G 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6346 (tppt) REVERT: I 89 ASP cc_start: 0.6369 (m-30) cc_final: 0.5967 (m-30) REVERT: I 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6345 (tppt) REVERT: M 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5962 (m-30) REVERT: M 119 LYS cc_start: 0.6842 (ttmm) cc_final: 0.6346 (tppt) REVERT: O 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5968 (m-30) REVERT: O 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6346 (tppt) REVERT: Q 89 ASP cc_start: 0.6372 (m-30) cc_final: 0.5967 (m-30) REVERT: Q 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6346 (tppt) REVERT: S 89 ASP cc_start: 0.6367 (m-30) cc_final: 0.5962 (m-30) REVERT: S 119 LYS cc_start: 0.6842 (ttmm) cc_final: 0.6346 (tppt) REVERT: U 89 ASP cc_start: 0.6369 (m-30) cc_final: 0.5966 (m-30) REVERT: U 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6345 (tppt) REVERT: W 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5961 (m-30) REVERT: W 119 LYS cc_start: 0.6842 (ttmm) cc_final: 0.6346 (tppt) REVERT: Y 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5968 (m-30) REVERT: Y 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6346 (tppt) REVERT: 2 89 ASP cc_start: 0.6369 (m-30) cc_final: 0.5966 (m-30) REVERT: 2 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6345 (tppt) REVERT: 4 89 ASP cc_start: 0.6372 (m-30) cc_final: 0.5967 (m-30) REVERT: 4 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6346 (tppt) REVERT: F 89 ASP cc_start: 0.6372 (m-30) cc_final: 0.5970 (m-30) REVERT: F 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6346 (tppt) REVERT: H 89 ASP cc_start: 0.6366 (m-30) cc_final: 0.5963 (m-30) REVERT: H 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6346 (tppt) REVERT: P 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5970 (m-30) REVERT: P 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6346 (tppt) REVERT: X 89 ASP cc_start: 0.6374 (m-30) cc_final: 0.5969 (m-30) REVERT: X 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6346 (tppt) REVERT: 6 89 ASP cc_start: 0.6373 (m-30) cc_final: 0.5969 (m-30) REVERT: 6 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6344 (tppt) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 1.4823 time to fit residues: 896.6945 Evaluate side-chains 503 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 250 optimal weight: 5.9990 chunk 267 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 86 GLN K 86 GLN a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 86 GLN G 86 GLN I 86 GLN M 86 GLN O 86 GLN Q 86 GLN S 86 GLN U 60 HIS U 86 GLN W 86 GLN Y 86 GLN 2 86 GLN 4 60 HIS 4 86 GLN F 86 GLN H 86 GLN P 86 GLN X 86 GLN 6 86 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38640 Z= 0.175 Angle : 0.631 10.675 52464 Z= 0.347 Chirality : 0.037 0.145 5400 Planarity : 0.004 0.057 7128 Dihedral : 4.692 19.916 5328 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 2.98 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.65 (0.11), residues: 5136 helix: 3.56 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.67 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP X 93 HIS 0.004 0.001 HIS B 60 PHE 0.020 0.003 PHE W 41 TYR 0.019 0.002 TYR W 39 ARG 0.011 0.001 ARG U 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 3.264 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 89 ASP cc_start: 0.6360 (m-30) cc_final: 0.5958 (m-30) REVERT: A 119 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6388 (tppt) REVERT: 1 89 ASP cc_start: 0.6361 (m-30) cc_final: 0.5956 (m-30) REVERT: 1 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6388 (tppt) REVERT: K 89 ASP cc_start: 0.6360 (m-30) cc_final: 0.5956 (m-30) REVERT: K 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6390 (tppt) REVERT: a 89 ASP cc_start: 0.6362 (m-30) cc_final: 0.5958 (m-30) REVERT: a 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6388 (tppt) REVERT: B 89 ASP cc_start: 0.6354 (m-30) cc_final: 0.5951 (m-30) REVERT: B 119 LYS cc_start: 0.6885 (ttmm) cc_final: 0.6390 (tppt) REVERT: E 89 ASP cc_start: 0.6354 (m-30) cc_final: 0.5951 (m-30) REVERT: E 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6389 (tppt) REVERT: e 89 ASP cc_start: 0.6360 (m-30) cc_final: 0.5958 (m-30) REVERT: e 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6389 (tppt) REVERT: r 89 ASP cc_start: 0.6362 (m-30) cc_final: 0.5958 (m-30) REVERT: r 119 LYS cc_start: 0.6879 (ttmm) cc_final: 0.6387 (tppt) REVERT: G 89 ASP cc_start: 0.6360 (m-30) cc_final: 0.5957 (m-30) REVERT: G 119 LYS cc_start: 0.6884 (ttmm) cc_final: 0.6390 (tppt) REVERT: I 89 ASP cc_start: 0.6358 (m-30) cc_final: 0.5957 (m-30) REVERT: I 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6388 (tppt) REVERT: M 89 ASP cc_start: 0.6354 (m-30) cc_final: 0.5950 (m-30) REVERT: M 119 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6389 (tppt) REVERT: O 89 ASP cc_start: 0.6361 (m-30) cc_final: 0.5957 (m-30) REVERT: O 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6389 (tppt) REVERT: Q 89 ASP cc_start: 0.6360 (m-30) cc_final: 0.5956 (m-30) REVERT: Q 119 LYS cc_start: 0.6884 (ttmm) cc_final: 0.6391 (tppt) REVERT: S 89 ASP cc_start: 0.6353 (m-30) cc_final: 0.5950 (m-30) REVERT: S 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6390 (tppt) REVERT: U 89 ASP cc_start: 0.6358 (m-30) cc_final: 0.5956 (m-30) REVERT: U 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6388 (tppt) REVERT: W 89 ASP cc_start: 0.6354 (m-30) cc_final: 0.5951 (m-30) REVERT: W 119 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6389 (tppt) REVERT: Y 89 ASP cc_start: 0.6360 (m-30) cc_final: 0.5956 (m-30) REVERT: Y 119 LYS cc_start: 0.6885 (ttmm) cc_final: 0.6391 (tppt) REVERT: 2 89 ASP cc_start: 0.6358 (m-30) cc_final: 0.5957 (m-30) REVERT: 2 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6388 (tppt) REVERT: 4 89 ASP cc_start: 0.6360 (m-30) cc_final: 0.5957 (m-30) REVERT: 4 119 LYS cc_start: 0.6884 (ttmm) cc_final: 0.6390 (tppt) REVERT: F 89 ASP cc_start: 0.6359 (m-30) cc_final: 0.5958 (m-30) REVERT: F 119 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6389 (tppt) REVERT: H 89 ASP cc_start: 0.6354 (m-30) cc_final: 0.5951 (m-30) REVERT: H 119 LYS cc_start: 0.6882 (ttmm) cc_final: 0.6388 (tppt) REVERT: P 89 ASP cc_start: 0.6362 (m-30) cc_final: 0.5958 (m-30) REVERT: P 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6389 (tppt) REVERT: X 89 ASP cc_start: 0.6361 (m-30) cc_final: 0.5958 (m-30) REVERT: X 119 LYS cc_start: 0.6881 (ttmm) cc_final: 0.6389 (tppt) REVERT: 6 89 ASP cc_start: 0.6362 (m-30) cc_final: 0.5958 (m-30) REVERT: 6 119 LYS cc_start: 0.6880 (ttmm) cc_final: 0.6388 (tppt) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 1.5034 time to fit residues: 908.3829 Evaluate side-chains 506 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 1.9990 chunk 376 optimal weight: 0.9980 chunk 343 optimal weight: 6.9990 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 287 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 331 optimal weight: 0.8980 chunk 346 optimal weight: 6.9990 chunk 365 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN 1 86 GLN K 86 GLN a 86 GLN B 86 GLN E 86 GLN e 86 GLN r 86 GLN G 86 GLN I 86 GLN M 86 GLN O 86 GLN Q 86 GLN S 86 GLN U 60 HIS U 86 GLN W 86 GLN Y 86 GLN 2 86 GLN 4 60 HIS 4 86 GLN F 86 GLN H 86 GLN P 86 GLN X 86 GLN 6 86 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 38640 Z= 0.159 Angle : 0.613 11.646 52464 Z= 0.336 Chirality : 0.037 0.145 5400 Planarity : 0.005 0.098 7128 Dihedral : 4.637 18.936 5328 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.79 % Allowed : 2.98 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.11), residues: 5136 helix: 3.67 (0.07), residues: 4176 sheet: None (None), residues: 0 loop : 0.71 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP X 93 HIS 0.005 0.001 HIS B 60 PHE 0.018 0.002 PHE 4 41 TYR 0.018 0.002 TYR a 39 ARG 0.013 0.001 ARG M 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 3.301 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: A 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5947 (m-30) REVERT: A 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6347 (tppt) REVERT: 1 89 ASP cc_start: 0.6332 (m-30) cc_final: 0.5946 (m-30) REVERT: 1 119 LYS cc_start: 0.6842 (ttmm) cc_final: 0.6346 (tppt) REVERT: K 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5946 (m-30) REVERT: K 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6348 (tppt) REVERT: a 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5946 (m-30) REVERT: a 119 LYS cc_start: 0.6840 (ttmm) cc_final: 0.6345 (tppt) REVERT: B 89 ASP cc_start: 0.6324 (m-30) cc_final: 0.5940 (m-30) REVERT: B 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6347 (tppt) REVERT: E 89 ASP cc_start: 0.6325 (m-30) cc_final: 0.5940 (m-30) REVERT: E 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6347 (tppt) REVERT: e 89 ASP cc_start: 0.6330 (m-30) cc_final: 0.5948 (m-30) REVERT: e 119 LYS cc_start: 0.6842 (ttmm) cc_final: 0.6347 (tppt) REVERT: r 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5946 (m-30) REVERT: r 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6345 (tppt) REVERT: G 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5946 (m-30) REVERT: G 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6348 (tppt) REVERT: I 89 ASP cc_start: 0.6328 (m-30) cc_final: 0.5945 (m-30) REVERT: I 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6346 (tppt) REVERT: M 89 ASP cc_start: 0.6323 (m-30) cc_final: 0.5939 (m-30) REVERT: M 119 LYS cc_start: 0.6842 (ttmm) cc_final: 0.6347 (tppt) REVERT: O 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5946 (m-30) REVERT: O 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6347 (tppt) REVERT: Q 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5946 (m-30) REVERT: Q 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6348 (tppt) REVERT: S 89 ASP cc_start: 0.6323 (m-30) cc_final: 0.5939 (m-30) REVERT: S 119 LYS cc_start: 0.6843 (ttmm) cc_final: 0.6348 (tppt) REVERT: U 89 ASP cc_start: 0.6328 (m-30) cc_final: 0.5945 (m-30) REVERT: U 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6346 (tppt) REVERT: W 89 ASP cc_start: 0.6323 (m-30) cc_final: 0.5939 (m-30) REVERT: W 119 LYS cc_start: 0.6842 (ttmm) cc_final: 0.6347 (tppt) REVERT: Y 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5946 (m-30) REVERT: Y 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6348 (tppt) REVERT: 2 89 ASP cc_start: 0.6328 (m-30) cc_final: 0.5945 (m-30) REVERT: 2 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6346 (tppt) REVERT: 4 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5946 (m-30) REVERT: 4 119 LYS cc_start: 0.6845 (ttmm) cc_final: 0.6348 (tppt) REVERT: F 89 ASP cc_start: 0.6329 (m-30) cc_final: 0.5947 (m-30) REVERT: F 119 LYS cc_start: 0.6845 (ttmm) cc_final: 0.6348 (tppt) REVERT: H 89 ASP cc_start: 0.6324 (m-30) cc_final: 0.5940 (m-30) REVERT: H 119 LYS cc_start: 0.6844 (ttmm) cc_final: 0.6346 (tppt) REVERT: P 89 ASP cc_start: 0.6332 (m-30) cc_final: 0.5947 (m-30) REVERT: P 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6346 (tppt) REVERT: X 89 ASP cc_start: 0.6332 (m-30) cc_final: 0.5946 (m-30) REVERT: X 119 LYS cc_start: 0.6842 (ttmm) cc_final: 0.6347 (tppt) REVERT: 6 89 ASP cc_start: 0.6331 (m-30) cc_final: 0.5946 (m-30) REVERT: 6 119 LYS cc_start: 0.6841 (ttmm) cc_final: 0.6345 (tppt) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 1.5436 time to fit residues: 937.2068 Evaluate side-chains 504 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.794 > 50: distance: 75 - 93: 11.072 distance: 79 - 100: 15.390 distance: 84 - 108: 6.868 distance: 88 - 93: 14.645 distance: 89 - 116: 3.262 distance: 89 - 127: 16.213 distance: 93 - 94: 9.024 distance: 94 - 95: 14.121 distance: 94 - 97: 25.610 distance: 95 - 96: 7.977 distance: 95 - 100: 15.826 distance: 96 - 138: 12.047 distance: 97 - 98: 30.807 distance: 97 - 99: 17.781 distance: 100 - 101: 30.700 distance: 101 - 102: 24.324 distance: 101 - 104: 29.824 distance: 102 - 103: 22.814 distance: 102 - 108: 22.982 distance: 103 - 147: 9.933 distance: 104 - 105: 32.142 distance: 105 - 106: 14.407 distance: 105 - 107: 10.623 distance: 108 - 109: 6.058 distance: 109 - 110: 19.698 distance: 109 - 112: 15.032 distance: 110 - 111: 10.401 distance: 110 - 116: 14.233 distance: 110 - 127: 29.198 distance: 111 - 155: 20.317 distance: 112 - 113: 3.760 distance: 113 - 114: 15.335 distance: 113 - 115: 17.469 distance: 116 - 117: 11.114 distance: 117 - 118: 9.542 distance: 117 - 120: 9.679 distance: 118 - 119: 9.680 distance: 118 - 138: 12.895 distance: 120 - 121: 12.648 distance: 121 - 122: 25.894 distance: 122 - 123: 32.847 distance: 123 - 124: 11.747 distance: 124 - 125: 26.774 distance: 124 - 126: 13.830 distance: 127 - 128: 13.518 distance: 128 - 129: 13.594 distance: 128 - 131: 8.537 distance: 129 - 130: 8.353 distance: 129 - 138: 25.658 distance: 131 - 132: 5.955 distance: 132 - 133: 14.668 distance: 133 - 134: 16.288 distance: 134 - 135: 8.828 distance: 135 - 136: 9.654 distance: 135 - 137: 4.974 distance: 138 - 139: 34.574 distance: 139 - 140: 34.248 distance: 139 - 142: 46.193 distance: 140 - 141: 6.824 distance: 140 - 147: 16.047 distance: 142 - 143: 45.066 distance: 143 - 144: 19.210 distance: 144 - 145: 11.718 distance: 145 - 146: 5.883 distance: 147 - 148: 16.894 distance: 148 - 149: 6.636 distance: 148 - 151: 20.210 distance: 149 - 150: 11.554 distance: 149 - 155: 12.387 distance: 151 - 152: 14.504 distance: 152 - 153: 21.871 distance: 153 - 154: 13.739 distance: 155 - 156: 6.017 distance: 156 - 157: 15.232 distance: 157 - 158: 15.022 distance: 157 - 159: 10.006 distance: 159 - 160: 18.424 distance: 160 - 161: 21.045 distance: 160 - 163: 46.100 distance: 161 - 162: 18.643 distance: 161 - 164: 6.703 distance: 164 - 165: 5.939 distance: 164 - 170: 31.634 distance: 165 - 166: 19.268 distance: 165 - 168: 27.622 distance: 166 - 167: 29.917 distance: 166 - 171: 19.581 distance: 166 - 180: 17.031 distance: 168 - 169: 22.406 distance: 169 - 170: 40.139 distance: 171 - 172: 21.639 distance: 172 - 173: 25.924 distance: 172 - 175: 8.432 distance: 173 - 174: 10.944 distance: 173 - 189: 24.852 distance: 175 - 176: 15.245 distance: 176 - 177: 17.047 distance: 177 - 178: 16.269 distance: 177 - 179: 26.203 distance: 180 - 181: 11.924 distance: 181 - 182: 10.316 distance: 181 - 184: 19.189 distance: 182 - 183: 15.265 distance: 182 - 195: 6.820 distance: 184 - 185: 12.861 distance: 185 - 186: 22.760 distance: 186 - 187: 30.318 distance: 186 - 188: 9.117