Starting phenix.real_space_refine on Tue Aug 26 12:49:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zg7_14705/08_2025/7zg7_14705.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zg7_14705/08_2025/7zg7_14705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zg7_14705/08_2025/7zg7_14705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zg7_14705/08_2025/7zg7_14705.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zg7_14705/08_2025/7zg7_14705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zg7_14705/08_2025/7zg7_14705.map" } resolution = 1.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 270 6.06 5 S 192 5.16 5 Na 112 4.78 5 C 22680 2.51 5 N 6264 2.21 5 O 9568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39086 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "B" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "C" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "D" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "E" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "F" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "G" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "H" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "I" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "J" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "K" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "L" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "M" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "N" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "O" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "P" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "Q" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "R" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "S" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "T" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "U" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "V" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "W" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "X" Number of atoms: 1501 Number of conformers: 4 Conformer: "A" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Conformer: "B" Number of residues, atoms: 172, 1413 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} bond proxies already assigned to first conformer: 1373 Conformer: "C" Number of residues, atoms: 172, 1360 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 10} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 1373 Conformer: "D" Number of residues, atoms: 172, 1350 Classifications: {'peptide': 172} Incomplete info: {'backbone_only': 12} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 bond proxies already assigned to first conformer: 1373 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' NA': 5, ' ZN': 12} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Unusual residues: {' NA': 4, ' ZN': 11} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' NA': 5, ' ZN': 13} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' NA': 5, ' ZN': 12} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "L" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Unusual residues: {' NA': 5, ' ZN': 12} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "M" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "O" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "Q" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "S" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "T" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "U" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "V" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Unusual residues: {' NA': 5, ' ZN': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "W" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Unusual residues: {' NA': 4, ' ZN': 10} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "C" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "D" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "E" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "F" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "G" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "H" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "J" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "K" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "L" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "M" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "N" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "O" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "P" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "Q" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "R" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "S" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "T" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "U" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "V" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "W" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "X" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Time building chain proxies: 28.55, per 1000 atoms: 0.73 Number of scatterers: 39086 At special positions: 0 Unit cell: (135.297, 136.202, 135.297, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 270 29.99 S 192 16.00 Na 112 11.00 O 9568 8.00 N 6264 7.00 C 22680 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: 3.58 Conformation dependent library (CDL) restraints added in 5.2 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 203 " pdb="ZN ZN A 203 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 203 " pdb="ZN ZN B 203 " - pdb=" ND1 HIS B 65 " pdb=" ZN C 203 " pdb="ZN ZN C 203 " - pdb=" ND1 HIS C 65 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" ND1 HIS D 65 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 65 " pdb=" ZN F 208 " pdb="ZN ZN F 208 " - pdb=" ND1 HIS F 65 " pdb=" ZN G 206 " pdb="ZN ZN G 206 " - pdb=" ND1 HIS G 65 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" ND1 HIS H 65 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 65 " pdb=" ZN J 207 " pdb="ZN ZN J 207 " - pdb=" ND1 HIS J 65 " pdb=" ZN K 206 " pdb="ZN ZN K 206 " - pdb=" ND1 HIS K 65 " pdb=" ZN L 202 " pdb="ZN ZN L 202 " - pdb=" ND1 HIS L 65 " pdb=" ZN M 206 " pdb="ZN ZN M 206 " - pdb=" ND1 HIS M 65 " pdb=" ZN N 207 " pdb="ZN ZN N 207 " - pdb=" ND1 HIS N 65 " pdb=" ZN O 206 " pdb="ZN ZN O 206 " - pdb=" ND1 HIS O 65 " pdb=" ZN P 207 " pdb="ZN ZN P 207 " - pdb=" ND1 HIS P 65 " pdb=" ZN Q 211 " pdb="ZN ZN Q 211 " - pdb=" ND1 HIS Q 65 " pdb=" ZN R 211 " pdb="ZN ZN R 211 " - pdb=" ND1 HIS R 65 " pdb=" ZN S 209 " pdb="ZN ZN S 209 " - pdb=" ND1 HIS S 65 " pdb=" ZN T 211 " pdb="ZN ZN T 211 " - pdb=" ND1 HIS T 65 " pdb=" ZN U 209 " pdb="ZN ZN U 209 " - pdb=" ND1 HIS U 65 " pdb=" ZN V 211 " pdb="ZN ZN V 211 " - pdb=" ND1 HIS V 65 " pdb=" ZN W 209 " pdb="ZN ZN W 209 " - pdb=" ND1 HIS W 65 " pdb=" ZN X 209 " pdb="ZN ZN X 209 " - pdb=" ND1 HIS X 65 " 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8736 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 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 Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 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 Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 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 Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 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 Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 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 Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 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 Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 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 Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 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 Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 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 Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 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 Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 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 Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 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 Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 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 Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 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 Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 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 Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 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 Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 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 2688 hydrogen bonds defined for protein. 8064 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: 7.72 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12090 1.34 - 1.46: 5053 1.46 - 1.57: 19313 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 36744 Sorted by residual: bond pdb=" C SER A 163 " pdb=" O SER A 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 1.03e+00 bond pdb=" C SER R 163 " pdb=" O SER R 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 9.86e-01 bond pdb=" C SER H 163 " pdb=" O SER H 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 9.86e-01 bond pdb=" C SER B 163 " pdb=" O SER B 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 9.86e-01 bond pdb=" C SER F 163 " pdb=" O SER F 163 " ideal model delta sigma weight residual 1.235 1.248 -0.012 1.23e-02 6.61e+03 9.86e-01 ... (remaining 36739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 46402 1.32 - 2.64: 2468 2.64 - 3.96: 402 3.96 - 5.28: 120 5.28 - 6.60: 72 Bond angle restraints: 49464 Sorted by residual: angle pdb=" C TRP V 93 " pdb=" N GLU V 94 " pdb=" CA GLU V 94 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C TRP B 93 " pdb=" N GLU B 94 " pdb=" CA GLU B 94 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C TRP N 93 " pdb=" N GLU N 94 " pdb=" CA GLU N 94 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C TRP K 93 " pdb=" N GLU K 94 " pdb=" CA GLU K 94 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 ... (remaining 49459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 20588 15.80 - 31.59: 1852 31.59 - 47.39: 432 47.39 - 63.18: 168 63.18 - 78.98: 72 Dihedral angle restraints: 23112 sinusoidal: 10032 harmonic: 13080 Sorted by residual: dihedral pdb=" CA VAL W 46 " pdb=" C VAL W 46 " pdb=" N ALA W 47 " pdb=" CA ALA W 47 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA VAL T 46 " pdb=" C VAL T 46 " pdb=" N ALA T 47 " pdb=" CA ALA T 47 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA VAL C 46 " pdb=" C VAL C 46 " pdb=" N ALA C 47 " pdb=" CA ALA C 47 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 23109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2951 0.026 - 0.053: 1496 0.053 - 0.079: 457 0.079 - 0.105: 308 0.105 - 0.132: 92 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA ILE V 80 " pdb=" N ILE V 80 " pdb=" C ILE V 80 " pdb=" CB ILE V 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE N 80 " pdb=" N ILE N 80 " pdb=" C ILE N 80 " pdb=" CB ILE N 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE W 80 " pdb=" N ILE W 80 " pdb=" C ILE W 80 " pdb=" CB ILE W 80 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 5301 not shown) Planarity restraints: 6408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 163 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C SER J 163 " -0.033 2.00e-02 2.50e+03 pdb=" O SER J 163 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY J 164 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 163 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C SER B 163 " 0.033 2.00e-02 2.50e+03 pdb=" O SER B 163 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY B 164 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER V 163 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C SER V 163 " -0.033 2.00e-02 2.50e+03 pdb=" O SER V 163 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY V 164 " 0.011 2.00e-02 2.50e+03 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 1054 2.54 - 3.13: 33170 3.13 - 3.72: 74240 3.72 - 4.31: 109338 4.31 - 4.90: 168897 Nonbonded interactions: 386699 Sorted by model distance: nonbonded pdb=" OE1 GLU E 62 " pdb="ZN ZN E 202 " model vdw 1.952 2.230 nonbonded pdb=" OE1 GLU P 62 " pdb="ZN ZN P 207 " model vdw 1.952 2.230 nonbonded pdb=" OE1 GLU K 62 " pdb="ZN ZN K 206 " model vdw 1.952 2.230 nonbonded pdb=" OE1 GLU R 62 " pdb="ZN ZN R 211 " model vdw 1.952 2.230 nonbonded pdb=" OE1 GLU C 62 " pdb="ZN ZN C 203 " model vdw 1.952 2.230 ... (remaining 386694 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 'A' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'B' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'C' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'D' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'E' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'F' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'G' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'H' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'I' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'J' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'K' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'L' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'M' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'N' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'O' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'P' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'Q' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'R' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'S' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'T' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'U' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'V' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'W' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) selection = (chain 'X' and (resid 5 through 13 or resid 15 through 33 or resid 35 through 48 \ or resid 50 through 52 or resid 54 through 60 or resid 62 or resid 65 through 9 \ 3 or resid 95 through 101 or resid 103 through 108 or resid 110 through 155 or r \ esid 157 through 161 or resid 163 through 171 or resid 173 through 176)) } 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=0.25 max=1.00 mean=0.95 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.540 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 67.350 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.004 0.027 36768 Z= 0.192 Angle : 0.740 6.596 49464 Z= 0.409 Chirality : 0.040 0.132 5304 Planarity : 0.005 0.030 6408 Dihedral : 14.441 78.980 14376 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.49 (0.13), residues: 4080 helix: 2.61 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.12 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG L 76 TYR 0.023 0.003 TYR R 39 PHE 0.028 0.004 PHE K 41 TRP 0.005 0.001 TRP N 93 HIS 0.005 0.002 HIS O 57 Details of bonding type rmsd covalent geometry : bond 0.00389 (36744) covalent geometry : angle 0.73982 (49464) hydrogen bonds : bond 0.07104 ( 2688) hydrogen bonds : angle 3.95381 ( 8064) metal coordination : bond 0.00100 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 1.741 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 1.0228 time to fit residues: 662.5154 Evaluate side-chains 487 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 50.0000 chunk 244 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS B 136 HIS D 136 HIS I 136 HIS J 136 HIS L 136 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.191907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.143245 restraints weight = 62237.482| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 0.59 r_work: 0.3120 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work: 0.2808 rms_B_bonded: 3.80 restraints_weight: 0.1250 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36768 Z= 0.154 Angle : 0.627 6.467 49464 Z= 0.340 Chirality : 0.037 0.142 5304 Planarity : 0.004 0.032 6408 Dihedral : 4.439 19.085 4560 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.37 % Allowed : 3.77 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.72 (0.13), residues: 4080 helix: 3.52 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 1.25 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG W 43 TYR 0.020 0.002 TYR S 39 PHE 0.021 0.003 PHE T 41 TRP 0.007 0.002 TRP W 93 HIS 0.004 0.001 HIS M 128 Details of bonding type rmsd covalent geometry : bond 0.00308 (36744) covalent geometry : angle 0.62702 (49464) hydrogen bonds : bond 0.05918 ( 2688) hydrogen bonds : angle 3.81872 ( 8064) metal coordination : bond 0.00083 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 538 time to evaluate : 1.029 Fit side-chains outliers start: 15 outliers final: 0 residues processed: 553 average time/residue: 0.7915 time to fit residues: 514.9295 Evaluate side-chains 485 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 48 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 341 optimal weight: 40.0000 chunk 87 optimal weight: 50.0000 chunk 19 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 304 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.191024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.139451 restraints weight = 61802.313| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 0.66 r_work: 0.3106 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work: 0.2804 rms_B_bonded: 3.72 restraints_weight: 0.1250 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36768 Z= 0.162 Angle : 0.645 6.636 49464 Z= 0.350 Chirality : 0.038 0.148 5304 Planarity : 0.004 0.029 6408 Dihedral : 4.417 18.950 4560 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.59 % Allowed : 3.70 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.96 (0.13), residues: 4080 helix: 3.76 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.05 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 76 TYR 0.022 0.002 TYR G 39 PHE 0.023 0.003 PHE B 41 TRP 0.008 0.002 TRP R 93 HIS 0.005 0.001 HIS A 136 Details of bonding type rmsd covalent geometry : bond 0.00331 (36744) covalent geometry : angle 0.64499 (49464) hydrogen bonds : bond 0.05967 ( 2688) hydrogen bonds : angle 3.85499 ( 8064) metal coordination : bond 0.00086 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 548 time to evaluate : 1.722 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 572 average time/residue: 0.8504 time to fit residues: 574.7964 Evaluate side-chains 479 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 479 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 249 optimal weight: 40.0000 chunk 52 optimal weight: 40.0000 chunk 231 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 170 optimal weight: 2.9990 chunk 358 optimal weight: 40.0000 chunk 71 optimal weight: 10.0000 chunk 147 optimal weight: 40.0000 chunk 140 optimal weight: 5.9990 chunk 179 optimal weight: 30.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS P 136 HIS Q 60 HIS Q 136 HIS R 60 HIS S 60 HIS S 136 HIS T 60 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.190085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.141273 restraints weight = 62662.464| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 0.55 r_work: 0.3117 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work: 0.2804 rms_B_bonded: 3.53 restraints_weight: 0.1250 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 36768 Z= 0.172 Angle : 0.668 6.795 49464 Z= 0.363 Chirality : 0.039 0.150 5304 Planarity : 0.005 0.033 6408 Dihedral : 4.430 18.564 4560 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.59 % Allowed : 4.12 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.87 (0.13), residues: 4080 helix: 3.70 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.02 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 76 TYR 0.023 0.003 TYR S 39 PHE 0.025 0.003 PHE O 41 TRP 0.008 0.002 TRP W 93 HIS 0.005 0.001 HIS S 136 Details of bonding type rmsd covalent geometry : bond 0.00356 (36744) covalent geometry : angle 0.66841 (49464) hydrogen bonds : bond 0.06111 ( 2688) hydrogen bonds : angle 3.88777 ( 8064) metal coordination : bond 0.00101 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 504 time to evaluate : 1.583 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 528 average time/residue: 0.8483 time to fit residues: 529.0304 Evaluate side-chains 495 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 480 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 119 LYS Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 19 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 394 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 171 optimal weight: 40.0000 chunk 22 optimal weight: 30.0000 chunk 334 optimal weight: 9.9990 chunk 405 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS G 60 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS M 136 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS R 136 HIS S 60 HIS T 60 HIS T 136 HIS U 60 HIS V 60 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.189927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.140116 restraints weight = 62739.911| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 0.60 r_work: 0.3105 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work: 0.2800 rms_B_bonded: 3.61 restraints_weight: 0.1250 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36768 Z= 0.175 Angle : 0.679 6.840 49464 Z= 0.368 Chirality : 0.039 0.152 5304 Planarity : 0.005 0.035 6408 Dihedral : 4.437 18.444 4560 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.59 % Allowed : 4.12 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.82 (0.13), residues: 4080 helix: 3.68 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.92 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG V 76 TYR 0.023 0.003 TYR U 39 PHE 0.025 0.003 PHE R 41 TRP 0.011 0.003 TRP K 93 HIS 0.006 0.002 HIS I 136 Details of bonding type rmsd covalent geometry : bond 0.00359 (36744) covalent geometry : angle 0.67876 (49464) hydrogen bonds : bond 0.06138 ( 2688) hydrogen bonds : angle 3.90287 ( 8064) metal coordination : bond 0.00112 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 504 time to evaluate : 1.204 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 528 average time/residue: 0.8156 time to fit residues: 508.2854 Evaluate side-chains 471 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 456 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 119 LYS Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 342 optimal weight: 50.0000 chunk 381 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 306 optimal weight: 30.0000 chunk 254 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 119 optimal weight: 50.0000 chunk 355 optimal weight: 8.9990 chunk 297 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS P 136 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS S 136 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.190795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.141181 restraints weight = 61939.008| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 0.64 r_work: 0.3132 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 2.31 restraints_weight: 0.2500 r_work: 0.2820 rms_B_bonded: 3.63 restraints_weight: 0.1250 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 36768 Z= 0.142 Angle : 0.597 6.795 49464 Z= 0.326 Chirality : 0.037 0.150 5304 Planarity : 0.004 0.025 6408 Dihedral : 4.407 18.767 4560 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.59 % Allowed : 4.09 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.05 (0.13), residues: 4080 helix: 3.84 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.98 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 76 TYR 0.021 0.002 TYR P 39 PHE 0.021 0.003 PHE J 41 TRP 0.012 0.003 TRP P 93 HIS 0.005 0.001 HIS P 105 Details of bonding type rmsd covalent geometry : bond 0.00274 (36744) covalent geometry : angle 0.59687 (49464) hydrogen bonds : bond 0.05729 ( 2688) hydrogen bonds : angle 3.78336 ( 8064) metal coordination : bond 0.00075 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 480 time to evaluate : 1.479 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 504 average time/residue: 0.7625 time to fit residues: 457.6882 Evaluate side-chains 464 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 447 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 119 LYS Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 280 optimal weight: 20.0000 chunk 185 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 311 optimal weight: 5.9990 chunk 344 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS G 60 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS R 136 HIS S 60 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.191831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.143247 restraints weight = 62405.787| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 0.62 r_work: 0.3146 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work: 0.2836 rms_B_bonded: 3.64 restraints_weight: 0.1250 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 36768 Z= 0.130 Angle : 0.569 6.722 49464 Z= 0.310 Chirality : 0.036 0.149 5304 Planarity : 0.004 0.021 6408 Dihedral : 4.362 18.987 4560 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.59 % Allowed : 4.34 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.20 (0.13), residues: 4080 helix: 3.97 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.93 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 76 TYR 0.020 0.002 TYR P 39 PHE 0.018 0.002 PHE I 41 TRP 0.013 0.003 TRP K 93 HIS 0.005 0.001 HIS H 105 Details of bonding type rmsd covalent geometry : bond 0.00245 (36744) covalent geometry : angle 0.56895 (49464) hydrogen bonds : bond 0.05483 ( 2688) hydrogen bonds : angle 3.70770 ( 8064) metal coordination : bond 0.00051 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 471 time to evaluate : 1.479 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 495 average time/residue: 0.8683 time to fit residues: 509.7655 Evaluate side-chains 463 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 439 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain G residue 119 LYS Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 119 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 119 LYS Chi-restraints excluded: chain U residue 119 LYS Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 372 optimal weight: 40.0000 chunk 174 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 350 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 181 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 40 optimal weight: 6.9990 chunk 297 optimal weight: 20.0000 chunk 87 optimal weight: 50.0000 chunk 142 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS H 60 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS S 136 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.190067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.140861 restraints weight = 62522.161| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 0.63 r_work: 0.3126 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.2809 rms_B_bonded: 3.57 restraints_weight: 0.1250 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 36768 Z= 0.159 Angle : 0.635 6.890 49464 Z= 0.346 Chirality : 0.038 0.150 5304 Planarity : 0.004 0.031 6408 Dihedral : 4.408 18.701 4560 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.59 % Allowed : 4.36 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.95 (0.13), residues: 4080 helix: 3.78 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.92 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG X 9 TYR 0.022 0.003 TYR U 39 PHE 0.024 0.003 PHE R 41 TRP 0.013 0.003 TRP W 93 HIS 0.004 0.001 HIS J 105 Details of bonding type rmsd covalent geometry : bond 0.00316 (36744) covalent geometry : angle 0.63475 (49464) hydrogen bonds : bond 0.05994 ( 2688) hydrogen bonds : angle 3.85729 ( 8064) metal coordination : bond 0.00117 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 480 time to evaluate : 1.488 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 504 average time/residue: 0.8941 time to fit residues: 534.8089 Evaluate side-chains 473 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 456 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 119 LYS Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 49 optimal weight: 10.0000 chunk 308 optimal weight: 50.0000 chunk 344 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 399 optimal weight: 4.9990 chunk 154 optimal weight: 40.0000 chunk 401 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS P 136 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS S 136 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.190550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.141152 restraints weight = 61597.811| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 0.63 r_work: 0.3117 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work: 0.2811 rms_B_bonded: 3.73 restraints_weight: 0.1250 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 36768 Z= 0.149 Angle : 0.617 7.008 49464 Z= 0.336 Chirality : 0.038 0.151 5304 Planarity : 0.004 0.028 6408 Dihedral : 4.406 18.541 4560 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.59 % Allowed : 4.51 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.97 (0.13), residues: 4080 helix: 3.80 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.92 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG X 9 TYR 0.022 0.002 TYR U 39 PHE 0.022 0.003 PHE R 41 TRP 0.017 0.004 TRP A 93 HIS 0.005 0.001 HIS V 105 Details of bonding type rmsd covalent geometry : bond 0.00292 (36744) covalent geometry : angle 0.61704 (49464) hydrogen bonds : bond 0.05848 ( 2688) hydrogen bonds : angle 3.81366 ( 8064) metal coordination : bond 0.00082 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 480 time to evaluate : 1.583 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 504 average time/residue: 0.9080 time to fit residues: 542.7081 Evaluate side-chains 473 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 456 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 119 LYS Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 148 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 161 optimal weight: 0.5980 chunk 63 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 338 optimal weight: 9.9990 chunk 353 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 319 optimal weight: 8.9990 chunk 301 optimal weight: 9.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS H 60 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS R 136 HIS S 60 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.190816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.142000 restraints weight = 60595.452| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 0.61 r_work: 0.3145 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 2.27 restraints_weight: 0.2500 r_work: 0.2823 rms_B_bonded: 3.59 restraints_weight: 0.1250 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 36768 Z= 0.145 Angle : 0.609 6.943 49464 Z= 0.332 Chirality : 0.037 0.150 5304 Planarity : 0.004 0.026 6408 Dihedral : 4.404 18.509 4560 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.56 % Allowed : 4.56 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.99 (0.13), residues: 4080 helix: 3.82 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.90 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 76 TYR 0.021 0.002 TYR N 39 PHE 0.021 0.003 PHE R 41 TRP 0.018 0.004 TRP W 93 HIS 0.004 0.001 HIS O 105 Details of bonding type rmsd covalent geometry : bond 0.00281 (36744) covalent geometry : angle 0.60909 (49464) hydrogen bonds : bond 0.05764 ( 2688) hydrogen bonds : angle 3.79254 ( 8064) metal coordination : bond 0.00079 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 480 time to evaluate : 1.467 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 503 average time/residue: 0.7759 time to fit residues: 463.4914 Evaluate side-chains 474 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 456 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 119 LYS Chi-restraints excluded: chain E residue 119 LYS Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain I residue 119 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 119 LYS Chi-restraints excluded: chain N residue 119 LYS Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain Q residue 119 LYS Chi-restraints excluded: chain R residue 119 LYS Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 119 LYS Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 119 LYS Chi-restraints excluded: chain X residue 119 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 139 optimal weight: 8.9990 chunk 154 optimal weight: 40.0000 chunk 142 optimal weight: 20.0000 chunk 248 optimal weight: 30.0000 chunk 274 optimal weight: 50.0000 chunk 331 optimal weight: 30.0000 chunk 105 optimal weight: 1.9990 chunk 199 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 136 HIS B 60 HIS B 136 HIS C 60 HIS C 136 HIS D 60 HIS D 136 HIS E 60 HIS E 136 HIS F 60 HIS F 136 HIS G 60 HIS G 136 HIS H 60 HIS H 136 HIS I 60 HIS I 136 HIS J 60 HIS J 136 HIS K 60 HIS K 136 HIS L 60 HIS L 136 HIS M 60 HIS M 136 HIS N 60 HIS N 136 HIS O 60 HIS O 136 HIS P 60 HIS P 136 HIS Q 60 HIS Q 136 HIS R 60 HIS R 136 HIS S 60 HIS S 136 HIS T 60 HIS T 136 HIS U 60 HIS U 136 HIS V 60 HIS V 136 HIS W 60 HIS W 136 HIS X 60 HIS X 136 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.191230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.141398 restraints weight = 62361.029| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 0.67 r_work: 0.3128 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work: 0.2823 rms_B_bonded: 3.72 restraints_weight: 0.1250 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 36768 Z= 0.139 Angle : 0.598 6.912 49464 Z= 0.325 Chirality : 0.037 0.150 5304 Planarity : 0.004 0.024 6408 Dihedral : 4.397 18.572 4560 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.44 % Allowed : 4.71 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.04 (0.13), residues: 4080 helix: 3.86 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.91 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG L 76 TYR 0.021 0.002 TYR K 39 PHE 0.020 0.003 PHE R 41 TRP 0.018 0.004 TRP W 93 HIS 0.005 0.001 HIS M 105 Details of bonding type rmsd covalent geometry : bond 0.00268 (36744) covalent geometry : angle 0.59800 (49464) hydrogen bonds : bond 0.05665 ( 2688) hydrogen bonds : angle 3.76399 ( 8064) metal coordination : bond 0.00069 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22838.22 seconds wall clock time: 388 minutes 8.02 seconds (23288.02 seconds total)