Starting phenix.real_space_refine on Tue Aug 26 13:20:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k3w_22658/08_2025/7k3w_22658.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k3w_22658/08_2025/7k3w_22658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k3w_22658/08_2025/7k3w_22658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k3w_22658/08_2025/7k3w_22658.map" model { file = "/net/cci-nas-00/data/ceres_data/7k3w_22658/08_2025/7k3w_22658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k3w_22658/08_2025/7k3w_22658.cif" } resolution = 1.36 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= 0.019 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 696 residue(s): 0.03s 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: 25.46, per 1000 atoms: 0.65 Number of scatterers: 39086 At special positions: 0 Unit cell: (136.042, 136.042, 136.042, 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: 3.60 Conformation dependent library (CDL) restraints added in 4.1 seconds Enol-peptide restraints added in 715.3 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: 0.98 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: 6.62 Time building geometry restraints manager: 4.46 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: 12072 1.34 - 1.46: 7632 1.46 - 1.58: 16752 1.58 - 1.70: 0 1.70 - 1.82: 288 Bond restraints: 36744 Sorted by residual: bond pdb=" CB PHE L 41 " pdb=" CG PHE L 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE N 41 " pdb=" CG PHE N 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE R 41 " pdb=" CG PHE R 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE F 41 " pdb=" CG PHE F 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 bond pdb=" CB PHE W 41 " pdb=" CG PHE W 41 " ideal model delta sigma weight residual 1.502 1.481 0.021 2.30e-02 1.89e+03 8.16e-01 ... (remaining 36739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 46008 1.36 - 2.71: 2904 2.71 - 4.07: 360 4.07 - 5.43: 120 5.43 - 6.79: 72 Bond angle restraints: 49464 Sorted by residual: angle pdb=" C TRP F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP I 93 " pdb=" N GLU I 94 " pdb=" CA GLU I 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP N 93 " pdb=" N GLU N 94 " pdb=" CA GLU N 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP S 93 " pdb=" N GLU S 94 " pdb=" CA GLU S 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C TRP W 93 " pdb=" N GLU W 94 " pdb=" CA GLU W 94 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 ... (remaining 49459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 22488 34.88 - 69.77: 432 69.77 - 104.65: 72 104.65 - 139.53: 24 139.53 - 174.42: 96 Dihedral angle restraints: 23112 sinusoidal: 10032 harmonic: 13080 Sorted by residual: dihedral pdb=" CB BGLU V 162 " pdb=" CG BGLU V 162 " pdb=" CD BGLU V 162 " pdb=" OE1BGLU V 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.42 -174.42 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB BGLU L 162 " pdb=" CG BGLU L 162 " pdb=" CD BGLU L 162 " pdb=" OE1BGLU L 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.42 -174.42 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB BGLU W 162 " pdb=" CG BGLU W 162 " pdb=" CD BGLU W 162 " pdb=" OE1BGLU W 162 " ideal model delta sinusoidal sigma weight residual 0.00 174.42 -174.42 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 23109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2688 0.026 - 0.052: 1656 0.052 - 0.078: 528 0.078 - 0.104: 216 0.104 - 0.130: 216 Chirality restraints: 5304 Sorted by residual: chirality pdb=" CA TYR V 39 " pdb=" N TYR V 39 " pdb=" C TYR V 39 " pdb=" CB TYR V 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA TYR G 39 " pdb=" N TYR G 39 " pdb=" C TYR G 39 " pdb=" CB TYR G 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 chirality pdb=" CA TYR I 39 " pdb=" N TYR I 39 " pdb=" C TYR I 39 " pdb=" CB TYR I 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 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 GLU C 94 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLU C 94 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU C 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER C 95 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 94 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLU B 94 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU B 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 95 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU S 94 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C GLU S 94 " 0.033 2.00e-02 2.50e+03 pdb=" O GLU S 94 " -0.012 2.00e-02 2.50e+03 pdb=" N SER S 95 " -0.011 2.00e-02 2.50e+03 ... (remaining 6405 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 720 2.53 - 3.12: 32688 3.12 - 3.71: 74220 3.71 - 4.31: 111552 4.31 - 4.90: 166356 Nonbonded interactions: 385536 Sorted by model distance: nonbonded pdb=" OE1 GLN O 112 " pdb="NA NA O 215 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN M 112 " pdb="NA NA M 215 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN H 112 " pdb="NA NA H 216 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN E 112 " pdb="NA NA E 215 " model vdw 1.934 2.470 nonbonded pdb=" OE1 GLN K 112 " pdb="NA NA K 215 " model vdw 1.934 2.470 ... (remaining 385531 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.860 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 60.020 Find NCS groups from input model: 1.070 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 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 : 0.005 0.064 36768 Z= 0.236 Angle : 0.757 6.786 49464 Z= 0.422 Chirality : 0.042 0.130 5304 Planarity : 0.004 0.033 6408 Dihedral : 20.576 174.417 14376 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 3.35 (0.13), residues: 4080 helix: 2.52 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.09 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 9 TYR 0.026 0.004 TYR R 39 PHE 0.023 0.004 PHE G 41 TRP 0.009 0.003 TRP V 93 HIS 0.008 0.002 HIS M 57 Details of bonding type rmsd covalent geometry : bond 0.00451 (36744) covalent geometry : angle 0.75723 (49464) hydrogen bonds : bond 0.10196 ( 2688) hydrogen bonds : angle 4.22012 ( 8064) metal coordination : bond 0.06427 ( 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 408 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.544 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.7673 time to fit residues: 380.9080 Evaluate side-chains 384 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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: 20.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.212362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144777 restraints weight = 48071.806| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 0.68 r_work: 0.3575 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work: 0.3241 rms_B_bonded: 3.31 restraints_weight: 0.1250 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 36768 Z= 0.260 Angle : 0.790 6.945 49464 Z= 0.433 Chirality : 0.043 0.139 5304 Planarity : 0.007 0.070 6408 Dihedral : 4.642 18.335 4560 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 3.45 (0.13), residues: 4080 helix: 2.58 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.15 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 79 TYR 0.026 0.004 TYR L 39 PHE 0.023 0.004 PHE A 41 TRP 0.009 0.003 TRP G 93 HIS 0.011 0.002 HIS N 57 Details of bonding type rmsd covalent geometry : bond 0.00525 (36744) covalent geometry : angle 0.79042 (49464) hydrogen bonds : bond 0.07797 ( 2688) hydrogen bonds : angle 4.15382 ( 8064) metal coordination : bond 0.00116 ( 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 408 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.441 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.7140 time to fit residues: 355.4729 Evaluate side-chains 384 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.365 ------------------------------------------------------------------------------- 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: 1.9990 chunk 40 optimal weight: 9.9990 chunk 341 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 253 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.214251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.147496 restraints weight = 48108.817| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 0.66 r_work: 0.3608 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work: 0.3277 rms_B_bonded: 3.31 restraints_weight: 0.1250 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 36768 Z= 0.161 Angle : 0.636 6.876 49464 Z= 0.346 Chirality : 0.038 0.140 5304 Planarity : 0.004 0.030 6408 Dihedral : 4.548 18.343 4560 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: 4.09 (0.13), residues: 4080 helix: 3.06 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.22 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 22 TYR 0.022 0.003 TYR K 39 PHE 0.017 0.003 PHE C 41 TRP 0.010 0.002 TRP V 93 HIS 0.005 0.001 HIS Q 57 Details of bonding type rmsd covalent geometry : bond 0.00309 (36744) covalent geometry : angle 0.63603 (49464) hydrogen bonds : bond 0.06564 ( 2688) hydrogen bonds : angle 3.92639 ( 8064) metal coordination : bond 0.00207 ( 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 432 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.442 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.7351 time to fit residues: 384.2973 Evaluate side-chains 384 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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: 30.0000 chunk 52 optimal weight: 20.0000 chunk 231 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 358 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 147 optimal weight: 30.0000 chunk 140 optimal weight: 4.9990 chunk 179 optimal weight: 0.5980 overall best weight: 4.9190 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.213358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.146125 restraints weight = 48733.820| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 0.67 r_work: 0.3591 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work: 0.3259 rms_B_bonded: 3.32 restraints_weight: 0.1250 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 36768 Z= 0.188 Angle : 0.682 7.040 49464 Z= 0.372 Chirality : 0.039 0.144 5304 Planarity : 0.005 0.048 6408 Dihedral : 4.589 17.858 4560 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 3.95 (0.13), residues: 4080 helix: 2.95 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.21 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 79 TYR 0.024 0.003 TYR N 39 PHE 0.019 0.003 PHE A 41 TRP 0.009 0.002 TRP D 93 HIS 0.006 0.001 HIS R 57 Details of bonding type rmsd covalent geometry : bond 0.00369 (36744) covalent geometry : angle 0.68161 (49464) hydrogen bonds : bond 0.06973 ( 2688) hydrogen bonds : angle 4.00411 ( 8064) metal coordination : bond 0.00207 ( 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 408 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.665 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.8032 time to fit residues: 398.8050 Evaluate side-chains 384 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 19 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 394 optimal weight: 7.9990 chunk 190 optimal weight: 0.8980 chunk 261 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 405 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.214155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147350 restraints weight = 49023.440| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 0.66 r_work: 0.3605 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.3276 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 36768 Z= 0.162 Angle : 0.634 6.960 49464 Z= 0.344 Chirality : 0.038 0.143 5304 Planarity : 0.004 0.034 6408 Dihedral : 4.539 18.105 4560 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 4.19 (0.13), residues: 4080 helix: 3.14 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.22 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 79 TYR 0.022 0.003 TYR W 39 PHE 0.017 0.003 PHE B 41 TRP 0.009 0.002 TRP V 93 HIS 0.004 0.001 HIS P 118 Details of bonding type rmsd covalent geometry : bond 0.00310 (36744) covalent geometry : angle 0.63367 (49464) hydrogen bonds : bond 0.06544 ( 2688) hydrogen bonds : angle 3.92381 ( 8064) metal coordination : bond 0.00210 ( 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 408 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.8084 time to fit residues: 401.2187 Evaluate side-chains 384 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 342 optimal weight: 6.9990 chunk 381 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 30.0000 chunk 306 optimal weight: 0.7980 chunk 254 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 40.0000 chunk 355 optimal weight: 0.7980 chunk 297 optimal weight: 0.9980 chunk 238 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.219615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154850 restraints weight = 49766.783| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 0.67 r_work: 0.3696 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 1.71 restraints_weight: 0.2500 r_work: 0.3383 rms_B_bonded: 3.38 restraints_weight: 0.1250 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 36768 Z= 0.111 Angle : 0.514 6.288 49464 Z= 0.275 Chirality : 0.034 0.139 5304 Planarity : 0.003 0.027 6408 Dihedral : 4.351 19.449 4560 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 5.03 (0.13), residues: 4080 helix: 3.75 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.38 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 22 TYR 0.017 0.002 TYR B 39 PHE 0.010 0.002 PHE S 41 TRP 0.010 0.002 TRP I 93 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00201 (36744) covalent geometry : angle 0.51428 (49464) hydrogen bonds : bond 0.04944 ( 2688) hydrogen bonds : angle 3.59336 ( 8064) metal coordination : bond 0.00185 ( 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 456 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.599 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.8791 time to fit residues: 480.1628 Evaluate side-chains 384 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 280 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 346 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 310 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.213787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.146646 restraints weight = 48546.878| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 0.67 r_work: 0.3601 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work: 0.3270 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.0588 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= 0.176 Angle : 0.651 6.820 49464 Z= 0.356 Chirality : 0.039 0.147 5304 Planarity : 0.005 0.043 6408 Dihedral : 4.567 18.432 4560 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 4.29 (0.13), residues: 4080 helix: 3.20 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.25 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 79 TYR 0.026 0.003 TYR I 39 PHE 0.020 0.003 PHE A 41 TRP 0.008 0.002 TRP V 93 HIS 0.005 0.001 HIS Q 57 Details of bonding type rmsd covalent geometry : bond 0.00345 (36744) covalent geometry : angle 0.65145 (49464) hydrogen bonds : bond 0.06751 ( 2688) hydrogen bonds : angle 3.95358 ( 8064) metal coordination : bond 0.00242 ( 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 456 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.408 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.7523 time to fit residues: 412.6690 Evaluate side-chains 432 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 372 optimal weight: 0.0870 chunk 174 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 350 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 181 optimal weight: 30.0000 chunk 123 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.214458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.147625 restraints weight = 48951.336| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 0.67 r_work: 0.3609 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.3281 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 36768 Z= 0.158 Angle : 0.630 6.870 49464 Z= 0.341 Chirality : 0.038 0.145 5304 Planarity : 0.004 0.034 6408 Dihedral : 4.557 18.644 4560 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 4.33 (0.13), residues: 4080 helix: 3.21 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.37 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 79 TYR 0.023 0.003 TYR C 39 PHE 0.017 0.003 PHE C 41 TRP 0.008 0.002 TRP I 93 HIS 0.004 0.001 HIS E 57 Details of bonding type rmsd covalent geometry : bond 0.00302 (36744) covalent geometry : angle 0.62986 (49464) hydrogen bonds : bond 0.06460 ( 2688) hydrogen bonds : angle 3.89986 ( 8064) metal coordination : bond 0.00219 ( 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 456 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.366 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.7725 time to fit residues: 422.3819 Evaluate side-chains 432 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 49 optimal weight: 20.0000 chunk 308 optimal weight: 7.9990 chunk 344 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 399 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 401 optimal weight: 1.9990 chunk 293 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.212867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.145665 restraints weight = 47722.090| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 0.66 r_work: 0.3589 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 1.68 restraints_weight: 0.2500 r_work: 0.3255 rms_B_bonded: 3.32 restraints_weight: 0.1250 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 36768 Z= 0.204 Angle : 0.697 7.015 49464 Z= 0.381 Chirality : 0.041 0.148 5304 Planarity : 0.006 0.060 6408 Dihedral : 4.624 17.937 4560 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 3.93 (0.13), residues: 4080 helix: 2.92 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.31 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG V 79 TYR 0.027 0.003 TYR K 39 PHE 0.020 0.004 PHE O 41 TRP 0.006 0.002 TRP L 93 HIS 0.006 0.002 HIS X 57 Details of bonding type rmsd covalent geometry : bond 0.00404 (36744) covalent geometry : angle 0.69700 (49464) hydrogen bonds : bond 0.07166 ( 2688) hydrogen bonds : angle 4.03161 ( 8064) metal coordination : bond 0.00199 ( 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 432 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.543 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.7846 time to fit residues: 408.5849 Evaluate side-chains 408 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 148 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 216 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 chunk 353 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 301 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.214730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148364 restraints weight = 47742.779| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 0.66 r_work: 0.3620 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work: 0.3291 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 36768 Z= 0.146 Angle : 0.604 6.842 49464 Z= 0.328 Chirality : 0.037 0.142 5304 Planarity : 0.004 0.028 6408 Dihedral : 4.542 18.576 4560 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 4.37 (0.13), residues: 4080 helix: 3.24 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.37 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 79 TYR 0.023 0.003 TYR T 39 PHE 0.016 0.003 PHE A 41 TRP 0.009 0.002 TRP V 93 HIS 0.004 0.001 HIS J 57 Details of bonding type rmsd covalent geometry : bond 0.00276 (36744) covalent geometry : angle 0.60429 (49464) hydrogen bonds : bond 0.06237 ( 2688) hydrogen bonds : angle 3.87505 ( 8064) metal coordination : bond 0.00171 ( 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 456 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.389 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.7836 time to fit residues: 429.2972 Evaluate side-chains 408 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 139 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 331 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.214011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.147131 restraints weight = 48708.779| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 0.67 r_work: 0.3606 rms_B_bonded: 1.08 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work: 0.3277 rms_B_bonded: 3.33 restraints_weight: 0.1250 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 120 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 36768 Z= 0.158 Angle : 0.623 6.947 49464 Z= 0.340 Chirality : 0.038 0.144 5304 Planarity : 0.005 0.039 6408 Dihedral : 4.557 18.483 4560 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 4.30 (0.13), residues: 4080 helix: 3.19 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 1.39 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 79 TYR 0.025 0.003 TYR N 39 PHE 0.018 0.003 PHE E 41 TRP 0.008 0.002 TRP I 93 HIS 0.004 0.001 HIS W 57 Details of bonding type rmsd covalent geometry : bond 0.00303 (36744) covalent geometry : angle 0.62335 (49464) hydrogen bonds : bond 0.06518 ( 2688) hydrogen bonds : angle 3.90831 ( 8064) metal coordination : bond 0.00225 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40475.57 seconds wall clock time: 684 minutes 1.62 seconds (41041.62 seconds total)