Starting phenix.real_space_refine on Fri Jan 16 13:32:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r5o_14332/01_2026/7r5o_14332.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r5o_14332/01_2026/7r5o_14332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r5o_14332/01_2026/7r5o_14332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r5o_14332/01_2026/7r5o_14332.map" model { file = "/net/cci-nas-00/data/ceres_data/7r5o_14332/01_2026/7r5o_14332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r5o_14332/01_2026/7r5o_14332.cif" } resolution = 1.58 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= 0.003 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: 5 Type Number sf(0) Gaussians S 192 5.16 5 Na 24 4.78 5 C 22032 2.51 5 N 6168 2.21 5 O 10104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 264 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38520 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "B" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "C" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "D" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "E" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "F" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "G" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "H" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "I" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "J" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "K" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "L" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "M" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "N" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "O" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "P" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "Q" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "R" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "S" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "T" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "U" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "V" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "W" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "X" Number of atoms: 1463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1399 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "B" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "E" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "F" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "G" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "H" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "I" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "J" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "K" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "L" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "M" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "N" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "O" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "P" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "Q" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "R" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "S" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "T" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "U" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "V" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "W" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "X" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Residues with excluded nonbonded symmetry interactions: 24 residue: pdb=" N ACYS A 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 102 " occ=0.50 residue: pdb=" N ACYS B 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 102 " occ=0.50 residue: pdb=" N ACYS C 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 102 " occ=0.50 residue: pdb=" N ACYS D 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 102 " occ=0.50 residue: pdb=" N ACYS E 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 102 " occ=0.50 residue: pdb=" N ACYS F 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 102 " occ=0.50 residue: pdb=" N ACYS G 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS G 102 " occ=0.50 residue: pdb=" N ACYS H 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 102 " occ=0.50 residue: pdb=" N ACYS I 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 102 " occ=0.50 residue: pdb=" N ACYS J 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 102 " occ=0.50 residue: pdb=" N ACYS K 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS K 102 " occ=0.50 residue: pdb=" N ACYS L 102 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS L 102 " occ=0.50 ... (remaining 12 not shown) Time building chain proxies: 15.77, per 1000 atoms: 0.41 Number of scatterers: 38520 At special positions: 0 Unit cell: (135.792, 135.792, 135.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 192 16.00 Na 24 11.00 O 10104 8.00 N 6168 7.00 C 22032 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: 3.75 Conformation dependent library (CDL) restraints added in 2.6 seconds 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8304 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 77 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 77 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 77 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 removed outlier: 3.527A pdb=" N GLU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 77 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 removed outlier: 3.528A pdb=" N GLU D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 77 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 77 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 77 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 3.527A pdb=" N GLU G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 77 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 77 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU I 167 " --> pdb=" O SER I 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 77 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 removed outlier: 3.528A pdb=" N GLU J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 77 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 3.527A pdb=" N GLU K 167 " --> pdb=" O SER K 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 77 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 removed outlier: 3.528A pdb=" N GLU L 167 " --> pdb=" O SER L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 77 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU M 167 " --> pdb=" O SER M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 77 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 removed outlier: 3.527A pdb=" N GLU N 167 " --> pdb=" O SER N 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 77 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 3.527A pdb=" N GLU O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 77 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU P 167 " --> pdb=" O SER P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 77 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 3.527A pdb=" N GLU Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 77 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU R 167 " --> pdb=" O SER R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 77 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU S 167 " --> pdb=" O SER S 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 77 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 removed outlier: 3.527A pdb=" N GLU T 167 " --> pdb=" O SER T 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 77 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 3.528A pdb=" N GLU U 167 " --> pdb=" O SER U 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 77 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 removed outlier: 3.527A pdb=" N GLU V 167 " --> pdb=" O SER V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 77 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 3.527A pdb=" N GLU W 167 " --> pdb=" O SER W 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 77 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 3.527A pdb=" N GLU X 167 " --> pdb=" O SER X 163 " (cutoff:3.500A) 2736 hydrogen bonds defined for protein. 8136 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: 8.99 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 6158 1.31 - 1.46: 11355 1.46 - 1.61: 18175 1.61 - 1.76: 0 1.76 - 1.90: 288 Bond restraints: 35976 Sorted by residual: bond pdb=" CG HIS I 65 " pdb=" ND1 HIS I 65 " ideal model delta sigma weight residual 1.378 1.445 -0.067 1.10e-02 8.26e+03 3.74e+01 bond pdb=" CG HIS M 65 " pdb=" ND1 HIS M 65 " ideal model delta sigma weight residual 1.378 1.445 -0.067 1.10e-02 8.26e+03 3.74e+01 bond pdb=" CG HIS O 65 " pdb=" ND1 HIS O 65 " ideal model delta sigma weight residual 1.378 1.445 -0.067 1.10e-02 8.26e+03 3.74e+01 bond pdb=" CG HIS S 65 " pdb=" ND1 HIS S 65 " ideal model delta sigma weight residual 1.378 1.445 -0.067 1.10e-02 8.26e+03 3.69e+01 bond pdb=" CG HIS H 65 " pdb=" ND1 HIS H 65 " ideal model delta sigma weight residual 1.378 1.445 -0.067 1.10e-02 8.26e+03 3.69e+01 ... (remaining 35971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 38055 2.45 - 4.90: 8822 4.90 - 7.36: 1507 7.36 - 9.81: 218 9.81 - 12.26: 46 Bond angle restraints: 48648 Sorted by residual: angle pdb=" CA PHE I 41 " pdb=" CB PHE I 41 " pdb=" CG PHE I 41 " ideal model delta sigma weight residual 113.80 105.58 8.22 1.00e+00 1.00e+00 6.76e+01 angle pdb=" CA PHE J 41 " pdb=" CB PHE J 41 " pdb=" CG PHE J 41 " ideal model delta sigma weight residual 113.80 105.58 8.22 1.00e+00 1.00e+00 6.76e+01 angle pdb=" CA PHE K 41 " pdb=" CB PHE K 41 " pdb=" CG PHE K 41 " ideal model delta sigma weight residual 113.80 105.58 8.22 1.00e+00 1.00e+00 6.76e+01 angle pdb=" CA PHE U 41 " pdb=" CB PHE U 41 " pdb=" CG PHE U 41 " ideal model delta sigma weight residual 113.80 105.58 8.22 1.00e+00 1.00e+00 6.76e+01 angle pdb=" CA PHE X 41 " pdb=" CB PHE X 41 " pdb=" CG PHE X 41 " ideal model delta sigma weight residual 113.80 105.58 8.22 1.00e+00 1.00e+00 6.76e+01 ... (remaining 48643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 21679 33.98 - 67.95: 473 67.95 - 101.93: 48 101.93 - 135.90: 0 135.90 - 169.88: 24 Dihedral angle restraints: 22224 sinusoidal: 9240 harmonic: 12984 Sorted by residual: dihedral pdb=" CB BGLU A 140 " pdb=" CG BGLU A 140 " pdb=" CD BGLU A 140 " pdb=" OE1BGLU A 140 " ideal model delta sinusoidal sigma weight residual 0.00 -169.88 169.88 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CB BGLU D 140 " pdb=" CG BGLU D 140 " pdb=" CD BGLU D 140 " pdb=" OE1BGLU D 140 " ideal model delta sinusoidal sigma weight residual 0.00 -169.83 169.83 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CB BGLU C 140 " pdb=" CG BGLU C 140 " pdb=" CD BGLU C 140 " pdb=" OE1BGLU C 140 " ideal model delta sinusoidal sigma weight residual 0.00 -169.83 169.83 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 22221 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.090: 877 0.090 - 0.180: 1652 0.180 - 0.270: 1528 0.270 - 0.359: 808 0.359 - 0.449: 223 Chirality restraints: 5088 Sorted by residual: chirality pdb=" CA ILE O 80 " pdb=" N ILE O 80 " pdb=" C ILE O 80 " pdb=" CB ILE O 80 " both_signs ideal model delta sigma weight residual False 2.43 2.88 -0.45 2.00e-01 2.50e+01 5.04e+00 chirality pdb=" CA ILE L 80 " pdb=" N ILE L 80 " pdb=" C ILE L 80 " pdb=" CB ILE L 80 " both_signs ideal model delta sigma weight residual False 2.43 2.88 -0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CA ILE E 80 " pdb=" N ILE E 80 " pdb=" C ILE E 80 " pdb=" CB ILE E 80 " both_signs ideal model delta sigma weight residual False 2.43 2.88 -0.45 2.00e-01 2.50e+01 5.01e+00 ... (remaining 5085 not shown) Planarity restraints: 6456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 34 " -0.098 2.00e-02 2.50e+03 5.86e-02 6.87e+01 pdb=" CG TYR M 34 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR M 34 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TYR M 34 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR M 34 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR M 34 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR M 34 " 0.037 2.00e-02 2.50e+03 pdb=" OH TYR M 34 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 34 " 0.098 2.00e-02 2.50e+03 5.85e-02 6.85e+01 pdb=" CG TYR J 34 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR J 34 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 TYR J 34 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR J 34 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR J 34 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR J 34 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR J 34 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 34 " 0.098 2.00e-02 2.50e+03 5.85e-02 6.85e+01 pdb=" CG TYR K 34 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR K 34 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 TYR K 34 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR K 34 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR K 34 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR K 34 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR K 34 " 0.085 2.00e-02 2.50e+03 ... (remaining 6453 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 645 2.52 - 3.11: 32498 3.11 - 3.71: 69029 3.71 - 4.30: 110772 4.30 - 4.90: 162154 Nonbonded interactions: 375098 Sorted by model distance: nonbonded pdb=" O HOH C 601 " pdb=" O HOH C 613 " model vdw 1.924 3.040 nonbonded pdb=" O HOH G 601 " pdb=" O HOH G 613 " model vdw 1.924 3.040 nonbonded pdb=" O HOH V 601 " pdb=" O HOH V 611 " model vdw 1.924 3.040 nonbonded pdb=" O HOH W 601 " pdb=" O HOH W 611 " model vdw 1.924 3.040 nonbonded pdb=" O HOH U 601 " pdb=" O HOH U 611 " model vdw 1.924 3.040 ... (remaining 375093 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'B' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'C' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'D' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'E' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'F' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'G' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'H' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'I' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'J' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'K' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'L' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'M' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'N' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'O' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'P' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'Q' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'R' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'S' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'T' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'U' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'V' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'W' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) selection = (chain 'X' and (resid 4 through 48 or resid 50 through 52 or resid 54 through 67 \ or resid 69 through 101 or resid 103 through 108 or resid 110 through 139 or re \ sid 141 through 155 or resid 157 through 500)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.97 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: 20.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 46.440 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 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 : 0.020 0.102 35976 Z= 1.118 Angle : 2.160 12.262 48648 Z= 1.401 Chirality : 0.213 0.449 5088 Planarity : 0.013 0.059 6456 Dihedral : 15.327 169.880 13920 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.62 % Allowed : 1.67 % Favored : 97.71 % Cbeta Deviations : 1.76 % 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 are not related in a simple way. whole: 1.54 (0.12), residues: 4248 helix: 1.32 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : -0.03 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.006 ARG B 79 TYR 0.098 0.025 TYR M 34 PHE 0.049 0.016 PHE Q 81 TRP 0.041 0.018 TRP F 93 HIS 0.036 0.011 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.01983 (35976) covalent geometry : angle 2.15967 (48648) hydrogen bonds : bond 0.13689 ( 2736) hydrogen bonds : angle 4.81137 ( 8136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 1.285 Fit side-chains REVERT: A 94 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7641 (tt0) REVERT: A 119 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8776 (tttm) REVERT: B 94 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7640 (tt0) REVERT: B 119 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8773 (tttm) REVERT: C 94 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7640 (tt0) REVERT: C 119 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8777 (tttm) REVERT: D 94 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7639 (tt0) REVERT: D 119 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8778 (tttm) REVERT: E 94 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7642 (tt0) REVERT: E 119 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8778 (tttm) REVERT: F 94 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7643 (tt0) REVERT: F 119 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8776 (tttm) REVERT: G 94 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7641 (tt0) REVERT: G 119 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8778 (tttm) REVERT: H 94 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7641 (tt0) REVERT: H 119 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8778 (tttm) REVERT: I 94 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7644 (tt0) REVERT: I 119 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8773 (tttm) REVERT: J 94 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7643 (tt0) REVERT: J 119 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8775 (tttm) REVERT: K 94 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7641 (tt0) REVERT: K 119 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8778 (tttm) REVERT: L 94 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7642 (tt0) REVERT: L 119 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8775 (tttm) REVERT: M 94 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7641 (tt0) REVERT: M 119 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8774 (tttm) REVERT: N 94 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7642 (tt0) REVERT: N 119 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8777 (tttm) REVERT: O 94 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7639 (tt0) REVERT: O 119 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8775 (tttm) REVERT: P 94 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7643 (tt0) REVERT: P 119 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8774 (tttm) REVERT: Q 94 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7638 (tt0) REVERT: Q 119 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8777 (tttm) REVERT: R 94 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7640 (tt0) REVERT: R 119 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8777 (tttm) REVERT: S 94 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7640 (tt0) REVERT: S 119 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8776 (tttm) REVERT: T 94 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7641 (tt0) REVERT: T 119 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8775 (tttm) REVERT: U 94 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7643 (tt0) REVERT: U 119 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8776 (tttm) REVERT: V 94 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7644 (tt0) REVERT: V 119 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8776 (tttm) REVERT: W 94 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7641 (tt0) REVERT: W 119 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8775 (tttm) REVERT: X 94 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7641 (tt0) REVERT: X 119 LYS cc_start: 0.9047 (ttmm) cc_final: 0.8776 (tttm) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 1.0536 time to fit residues: 605.6762 Evaluate side-chains 456 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.5980 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 139 ASN B 98 ASN B 139 ASN C 98 ASN C 139 ASN D 98 ASN D 139 ASN E 98 ASN E 139 ASN F 98 ASN F 139 ASN G 98 ASN G 139 ASN H 98 ASN H 139 ASN I 98 ASN I 139 ASN J 98 ASN J 139 ASN K 98 ASN K 139 ASN L 98 ASN L 139 ASN M 98 ASN M 139 ASN N 98 ASN N 139 ASN O 98 ASN O 139 ASN P 98 ASN P 139 ASN Q 98 ASN Q 139 ASN R 98 ASN R 139 ASN S 98 ASN S 139 ASN T 98 ASN T 139 ASN U 98 ASN U 109 ASN A U 139 ASN V 98 ASN V 139 ASN W 98 ASN W 109 ASN A W 139 ASN X 98 ASN X 109 ASN A X 139 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.132844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.108884 restraints weight = 159016.631| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.68 r_work: 0.2910 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 35976 Z= 0.140 Angle : 0.592 5.783 48648 Z= 0.321 Chirality : 0.037 0.151 5088 Planarity : 0.003 0.024 6456 Dihedral : 4.683 26.183 4896 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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 are not related in a simple way. whole: 4.40 (0.12), residues: 4248 helix: 3.35 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.64 (0.25), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 63 TYR 0.016 0.003 TYR I 39 PHE 0.014 0.002 PHE P 41 TRP 0.016 0.003 TRP L 93 HIS 0.003 0.001 HIS O 60 Details of bonding type rmsd covalent geometry : bond 0.00257 (35976) covalent geometry : angle 0.59159 (48648) hydrogen bonds : bond 0.06588 ( 2736) hydrogen bonds : angle 3.66618 ( 8136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.368 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 552 average time/residue: 0.9440 time to fit residues: 602.7609 Evaluate side-chains 516 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 127 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 284 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 353 optimal weight: 2.9990 chunk 221 optimal weight: 0.0470 chunk 307 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A C 109 ASN A E 109 ASN A H 109 ASN A I 109 ASN A M 109 ASN A P 109 ASN A Q 109 ASN A R 109 ASN A S 109 ASN A T 109 ASN A V 109 ASN A Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109993 restraints weight = 150265.422| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.06 r_work: 0.2934 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 35976 Z= 0.131 Angle : 0.555 5.502 48648 Z= 0.298 Chirality : 0.037 0.148 5088 Planarity : 0.003 0.020 6456 Dihedral : 4.440 20.591 4896 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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 are not related in a simple way. whole: 5.14 (0.12), residues: 4248 helix: 3.87 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.86 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 79 TYR 0.016 0.002 TYR X 39 PHE 0.013 0.002 PHE I 41 TRP 0.013 0.003 TRP P 93 HIS 0.003 0.001 HIS F 128 Details of bonding type rmsd covalent geometry : bond 0.00235 (35976) covalent geometry : angle 0.55456 (48648) hydrogen bonds : bond 0.06267 ( 2736) hydrogen bonds : angle 3.61816 ( 8136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.474 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 0.9927 time to fit residues: 603.4274 Evaluate side-chains 523 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 170 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 360 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 329 optimal weight: 0.7980 chunk 385 optimal weight: 0.5980 chunk 232 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 ASN A G 109 ASN A N 109 ASN A O 109 ASN A Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.109227 restraints weight = 158622.351| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.09 r_work: 0.2916 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 35976 Z= 0.137 Angle : 0.567 5.649 48648 Z= 0.304 Chirality : 0.037 0.149 5088 Planarity : 0.003 0.020 6456 Dihedral : 4.410 20.643 4896 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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 are not related in a simple way. whole: 5.17 (0.12), residues: 4248 helix: 3.89 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.89 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 79 TYR 0.016 0.002 TYR V 39 PHE 0.014 0.002 PHE L 41 TRP 0.015 0.003 TRP T 93 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00251 (35976) covalent geometry : angle 0.56702 (48648) hydrogen bonds : bond 0.06400 ( 2736) hydrogen bonds : angle 3.65123 ( 8136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 1.420 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 1.0114 time to fit residues: 611.4090 Evaluate side-chains 526 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 247 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 272 optimal weight: 0.4980 chunk 330 optimal weight: 0.9990 chunk 208 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 395 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.132483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.109375 restraints weight = 150661.397| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.28 r_work: 0.2896 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 35976 Z= 0.143 Angle : 0.577 5.763 48648 Z= 0.310 Chirality : 0.038 0.150 5088 Planarity : 0.003 0.019 6456 Dihedral : 4.398 20.459 4896 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 0.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: 5.16 (0.12), residues: 4248 helix: 3.87 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.91 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 79 TYR 0.017 0.002 TYR W 39 PHE 0.015 0.002 PHE D 41 TRP 0.015 0.003 TRP X 93 HIS 0.003 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00267 (35976) covalent geometry : angle 0.57724 (48648) hydrogen bonds : bond 0.06570 ( 2736) hydrogen bonds : angle 3.67742 ( 8136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.399 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 1.0403 time to fit residues: 597.9092 Evaluate side-chains 492 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 492 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 368 optimal weight: 4.9990 chunk 340 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 323 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 287 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 109 ASN A Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.131315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107783 restraints weight = 152918.818| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.07 r_work: 0.2888 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 35976 Z= 0.161 Angle : 0.615 6.107 48648 Z= 0.332 Chirality : 0.039 0.154 5088 Planarity : 0.003 0.018 6456 Dihedral : 4.456 20.402 4896 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 0.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: 4.98 (0.12), residues: 4248 helix: 3.75 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.85 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 79 TYR 0.020 0.002 TYR H 39 PHE 0.018 0.003 PHE V 41 TRP 0.015 0.004 TRP X 93 HIS 0.004 0.001 HIS M 128 Details of bonding type rmsd covalent geometry : bond 0.00315 (35976) covalent geometry : angle 0.61507 (48648) hydrogen bonds : bond 0.07032 ( 2736) hydrogen bonds : angle 3.77497 ( 8136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.469 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 1.0413 time to fit residues: 597.2431 Evaluate side-chains 503 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 267 optimal weight: 1.9990 chunk 333 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 255 optimal weight: 0.1980 chunk 323 optimal weight: 8.9990 chunk 361 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 392 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 86 GLN B 109 ASN A C 86 GLN F 86 GLN G 86 GLN H 86 GLN M 86 GLN N 86 GLN Q 86 GLN R 86 GLN S 86 GLN T 86 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.133525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110527 restraints weight = 150403.826| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.35 r_work: 0.2916 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 35976 Z= 0.134 Angle : 0.557 5.732 48648 Z= 0.299 Chirality : 0.037 0.152 5088 Planarity : 0.003 0.017 6456 Dihedral : 4.331 20.101 4896 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: 5.24 (0.12), residues: 4248 helix: 3.93 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.95 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 79 TYR 0.018 0.002 TYR H 39 PHE 0.014 0.002 PHE P 41 TRP 0.017 0.004 TRP T 93 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00247 (35976) covalent geometry : angle 0.55733 (48648) hydrogen bonds : bond 0.06221 ( 2736) hydrogen bonds : angle 3.61426 ( 8136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 528 time to evaluate : 1.510 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 528 average time/residue: 1.0148 time to fit residues: 616.9047 Evaluate side-chains 488 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 354 optimal weight: 7.9990 chunk 268 optimal weight: 0.5980 chunk 342 optimal weight: 2.9990 chunk 383 optimal weight: 0.9980 chunk 341 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108894 restraints weight = 157648.272| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.13 r_work: 0.2902 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 35976 Z= 0.146 Angle : 0.586 5.934 48648 Z= 0.314 Chirality : 0.038 0.151 5088 Planarity : 0.003 0.017 6456 Dihedral : 4.375 20.079 4896 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: 5.14 (0.12), residues: 4248 helix: 3.85 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.95 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 79 TYR 0.018 0.002 TYR W 39 PHE 0.016 0.002 PHE I 41 TRP 0.018 0.004 TRP X 93 HIS 0.004 0.001 HIS S 128 Details of bonding type rmsd covalent geometry : bond 0.00277 (35976) covalent geometry : angle 0.58568 (48648) hydrogen bonds : bond 0.06640 ( 2736) hydrogen bonds : angle 3.68667 ( 8136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 1.326 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 1.0575 time to fit residues: 581.2643 Evaluate side-chains 482 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 396 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 397 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 379 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 327 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.106589 restraints weight = 157316.515| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.24 r_work: 0.2846 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 35976 Z= 0.187 Angle : 0.662 6.586 48648 Z= 0.359 Chirality : 0.041 0.155 5088 Planarity : 0.004 0.018 6456 Dihedral : 4.493 20.116 4896 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: 4.81 (0.12), residues: 4248 helix: 3.63 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.77 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 79 TYR 0.021 0.003 TYR Q 39 PHE 0.020 0.003 PHE U 41 TRP 0.016 0.005 TRP N 93 HIS 0.005 0.002 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00380 (35976) covalent geometry : angle 0.66230 (48648) hydrogen bonds : bond 0.07500 ( 2736) hydrogen bonds : angle 3.86110 ( 8136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 475 time to evaluate : 1.413 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 1.0672 time to fit residues: 579.3940 Evaluate side-chains 476 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 359 optimal weight: 0.6980 chunk 355 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 333 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 312 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109673 restraints weight = 154095.061| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.39 r_work: 0.2897 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 35976 Z= 0.140 Angle : 0.575 5.934 48648 Z= 0.309 Chirality : 0.038 0.150 5088 Planarity : 0.003 0.017 6456 Dihedral : 4.383 19.927 4896 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % 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 are not related in a simple way. whole: 5.11 (0.12), residues: 4248 helix: 3.84 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.88 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG T 79 TYR 0.018 0.002 TYR B 39 PHE 0.015 0.002 PHE T 41 TRP 0.022 0.005 TRP S 93 HIS 0.004 0.001 HIS K 128 Details of bonding type rmsd covalent geometry : bond 0.00262 (35976) covalent geometry : angle 0.57492 (48648) hydrogen bonds : bond 0.06450 ( 2736) hydrogen bonds : angle 3.66701 ( 8136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8496 Ramachandran restraints generated. 4248 Oldfield, 0 Emsley, 4248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 484 time to evaluate : 1.405 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 1.0782 time to fit residues: 594.9839 Evaluate side-chains 480 residues out of total 3504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 67 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 386 optimal weight: 3.9990 chunk 330 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 373 optimal weight: 0.9980 chunk 346 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109285 restraints weight = 151102.064| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.29 r_work: 0.2897 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 35976 Z= 0.144 Angle : 0.582 5.991 48648 Z= 0.313 Chirality : 0.038 0.151 5088 Planarity : 0.003 0.017 6456 Dihedral : 4.380 19.682 4896 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.11 (0.12), residues: 4248 helix: 3.84 (0.08), residues: 3480 sheet: None (None), residues: 0 loop : 0.91 (0.26), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 79 TYR 0.017 0.002 TYR U 39 PHE 0.015 0.002 PHE U 41 TRP 0.025 0.006 TRP R 93 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00271 (35976) covalent geometry : angle 0.58244 (48648) hydrogen bonds : bond 0.06578 ( 2736) hydrogen bonds : angle 3.68492 ( 8136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26550.64 seconds wall clock time: 450 minutes 3.87 seconds (27003.87 seconds total)