Starting phenix.real_space_refine on Fri Feb 6 23:08:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zc2_74020/02_2026/9zc2_74020.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zc2_74020/02_2026/9zc2_74020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9zc2_74020/02_2026/9zc2_74020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zc2_74020/02_2026/9zc2_74020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9zc2_74020/02_2026/9zc2_74020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zc2_74020/02_2026/9zc2_74020.map" } resolution = 1.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 12 7.16 5 S 36 5.16 5 C 9072 2.51 5 N 2388 2.21 5 O 4032 1.98 5 H 13440 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28980 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "B" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "C" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "D" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "E" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "F" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "G" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "H" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "I" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "J" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "K" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "L" Number of atoms: 2307 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Conformer: "B" Number of residues, atoms: 154, 2226 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Conformer: "C" Number of residues, atoms: 154, 2169 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 151} Unresolved chain link angles: 10 Unresolved chain link dihedrals: 20 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 bond proxies already assigned to first conformer: 2168 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "C" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "E" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "F" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "G" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "H" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "I" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "K" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} Chain: "L" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Residues with excluded nonbonded symmetry interactions: 36 residue: pdb=" O HOH A 401 " occ=0.33 residue: pdb=" O HOH A 494 " occ=0.33 residue: pdb=" O HOH A 495 " occ=0.33 residue: pdb=" O HOH B 401 " occ=0.33 residue: pdb=" O HOH B 411 " occ=0.33 residue: pdb=" O HOH B 495 " occ=0.33 residue: pdb=" O HOH C 401 " occ=0.33 residue: pdb=" O HOH C 404 " occ=0.33 residue: pdb=" O HOH C 495 " occ=0.33 residue: pdb=" O HOH D 401 " occ=0.33 residue: pdb=" O HOH D 495 " occ=0.33 residue: pdb=" O HOH D 503 " occ=0.33 ... (remaining 24 not shown) Time building chain proxies: 12.89, per 1000 atoms: 0.44 Number of scatterers: 28980 At special positions: 0 Unit cell: (106.481, 99.626, 95.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 12 26.01 S 36 16.00 O 4032 8.00 N 2388 7.00 C 9072 6.00 H 13440 1.00 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: 2.81 Conformation dependent library (CDL) restraints added in 2.1 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3768 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 22 through 54 Processing helix chain 'A' and resid 58 through 87 removed outlier: 3.766A pdb=" N ASP A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 113 through 139 removed outlier: 4.247A pdb=" N GLY A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 165 Processing helix chain 'B' and resid 22 through 54 Processing helix chain 'B' and resid 58 through 87 removed outlier: 3.743A pdb=" N ASP B 67 " --> pdb=" O HIS B 63 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 Processing helix chain 'B' and resid 113 through 139 removed outlier: 4.258A pdb=" N GLY B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 Processing helix chain 'C' and resid 22 through 54 Processing helix chain 'C' and resid 58 through 87 removed outlier: 3.757A pdb=" N ASP C 67 " --> pdb=" O HIS C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 113 through 139 removed outlier: 4.238A pdb=" N GLY C 137 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 165 Processing helix chain 'D' and resid 22 through 54 Processing helix chain 'D' and resid 58 through 87 removed outlier: 3.732A pdb=" N ASP D 67 " --> pdb=" O HIS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 113 through 139 removed outlier: 4.231A pdb=" N GLY D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 165 Processing helix chain 'E' and resid 22 through 54 Processing helix chain 'E' and resid 58 through 87 removed outlier: 3.732A pdb=" N ASP E 67 " --> pdb=" O HIS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 102 Processing helix chain 'E' and resid 113 through 139 removed outlier: 4.215A pdb=" N GLY E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 165 Processing helix chain 'F' and resid 22 through 54 Processing helix chain 'F' and resid 58 through 87 removed outlier: 3.756A pdb=" N ASP F 67 " --> pdb=" O HIS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 102 Processing helix chain 'F' and resid 113 through 139 removed outlier: 4.201A pdb=" N GLY F 137 " --> pdb=" O ARG F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 165 Processing helix chain 'G' and resid 22 through 54 Processing helix chain 'G' and resid 58 through 87 removed outlier: 3.736A pdb=" N ASP G 67 " --> pdb=" O HIS G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 102 Processing helix chain 'G' and resid 113 through 139 removed outlier: 4.222A pdb=" N GLY G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 165 Processing helix chain 'H' and resid 22 through 54 Processing helix chain 'H' and resid 58 through 87 removed outlier: 3.745A pdb=" N ASP H 67 " --> pdb=" O HIS H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 102 Processing helix chain 'H' and resid 113 through 139 removed outlier: 4.248A pdb=" N GLY H 137 " --> pdb=" O ARG H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 165 Processing helix chain 'I' and resid 22 through 54 Processing helix chain 'I' and resid 58 through 87 removed outlier: 3.741A pdb=" N ASP I 67 " --> pdb=" O HIS I 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'I' and resid 113 through 139 removed outlier: 4.245A pdb=" N GLY I 137 " --> pdb=" O ARG I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 165 Processing helix chain 'J' and resid 22 through 54 Processing helix chain 'J' and resid 58 through 87 removed outlier: 3.726A pdb=" N ASP J 67 " --> pdb=" O HIS J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 102 Processing helix chain 'J' and resid 113 through 139 removed outlier: 4.206A pdb=" N GLY J 137 " --> pdb=" O ARG J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 165 Processing helix chain 'K' and resid 22 through 54 Processing helix chain 'K' and resid 58 through 87 removed outlier: 3.759A pdb=" N ASP K 67 " --> pdb=" O HIS K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 102 Processing helix chain 'K' and resid 113 through 139 removed outlier: 4.182A pdb=" N GLY K 137 " --> pdb=" O ARG K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 165 Processing helix chain 'L' and resid 22 through 54 Processing helix chain 'L' and resid 58 through 87 removed outlier: 3.740A pdb=" N ASP L 67 " --> pdb=" O HIS L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 102 Processing helix chain 'L' and resid 113 through 139 removed outlier: 4.177A pdb=" N GLY L 137 " --> pdb=" O ARG L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 165 1221 hydrogen bonds defined for protein. 3603 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 13440 1.03 - 1.22: 0 1.22 - 1.42: 5916 1.42 - 1.61: 8580 1.61 - 1.81: 72 Bond restraints: 28008 Sorted by residual: bond pdb=" N LEU J 14 " pdb=" CA LEU J 14 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.69e+00 bond pdb=" N LEU G 14 " pdb=" CA LEU G 14 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" N LEU B 14 " pdb=" CA LEU B 14 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.55e+00 bond pdb=" N LEU D 14 " pdb=" CA LEU D 14 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" N LEU H 14 " pdb=" CA LEU H 14 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.50e+00 ... (remaining 28003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.90: 44539 0.90 - 1.81: 5475 1.81 - 2.71: 333 2.71 - 3.61: 46 3.61 - 4.52: 31 Bond angle restraints: 50424 Sorted by residual: angle pdb=" N HIS D 51 " pdb=" CA HIS D 51 " pdb=" CB HIS D 51 " ideal model delta sigma weight residual 110.12 107.32 2.80 1.47e+00 4.63e-01 3.63e+00 angle pdb=" N HIS G 51 " pdb=" CA HIS G 51 " pdb=" CB HIS G 51 " ideal model delta sigma weight residual 110.12 107.32 2.80 1.47e+00 4.63e-01 3.62e+00 angle pdb=" CA HIS D 51 " pdb=" CB HIS D 51 " pdb=" CG HIS D 51 " ideal model delta sigma weight residual 113.80 115.66 -1.86 1.00e+00 1.00e+00 3.46e+00 angle pdb=" CA HIS G 51 " pdb=" CB HIS G 51 " pdb=" CG HIS G 51 " ideal model delta sigma weight residual 113.80 115.66 -1.86 1.00e+00 1.00e+00 3.45e+00 angle pdb=" CA HIS F 51 " pdb=" CB HIS F 51 " pdb=" CG HIS F 51 " ideal model delta sigma weight residual 113.80 115.65 -1.85 1.00e+00 1.00e+00 3.43e+00 ... (remaining 50419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.46: 11916 13.46 - 26.93: 1061 26.93 - 40.39: 302 40.39 - 53.86: 93 53.86 - 67.32: 68 Dihedral angle restraints: 13440 sinusoidal: 6816 harmonic: 6624 Sorted by residual: dihedral pdb=" CA TRP H 52 " pdb=" C TRP H 52 " pdb=" N ASN H 53 " pdb=" CA ASN H 53 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA TRP B 52 " pdb=" C TRP B 52 " pdb=" N ASN B 53 " pdb=" CA ASN B 53 " ideal model delta harmonic sigma weight residual -180.00 -159.36 -20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA TRP C 52 " pdb=" C TRP C 52 " pdb=" N ASN C 53 " pdb=" CA ASN C 53 " ideal model delta harmonic sigma weight residual -180.00 -159.62 -20.38 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 13437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1536 0.025 - 0.050: 546 0.050 - 0.075: 277 0.075 - 0.100: 139 0.100 - 0.126: 22 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA VAL J 90 " pdb=" N VAL J 90 " pdb=" C VAL J 90 " pdb=" CB VAL J 90 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA VAL L 90 " pdb=" N VAL L 90 " pdb=" C VAL L 90 " pdb=" CB VAL L 90 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL C 90 " pdb=" N VAL C 90 " pdb=" C VAL C 90 " pdb=" CB VAL C 90 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 2517 not shown) Planarity restraints: 4332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 51 " -0.017 2.00e-02 2.50e+03 1.16e-02 3.04e+00 pdb=" CG HIS B 51 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS B 51 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS B 51 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 51 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS B 51 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS B 51 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS B 51 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS B 51 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 51 " 0.017 2.00e-02 2.50e+03 1.14e-02 2.91e+00 pdb=" CG HIS F 51 " -0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS F 51 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS F 51 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS F 51 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 HIS F 51 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 HIS F 51 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 HIS F 51 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 HIS F 51 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 51 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.85e+00 pdb=" CG HIS A 51 " -0.027 2.00e-02 2.50e+03 pdb=" ND1 HIS A 51 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 51 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS A 51 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 51 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS A 51 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 HIS A 51 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 HIS A 51 " 0.003 2.00e-02 2.50e+03 ... (remaining 4329 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 2492 2.22 - 2.82: 62906 2.82 - 3.41: 89055 3.41 - 4.01: 125251 4.01 - 4.60: 189483 Nonbonded interactions: 469187 Sorted by model distance: nonbonded pdb="HE21 GLN C 36 " pdb=" O HOH C 403 " model vdw 1.630 2.450 nonbonded pdb="HE21 GLN K 36 " pdb=" O HOH K 404 " model vdw 1.633 2.450 nonbonded pdb="HE21 GLN J 36 " pdb=" O HOH J 405 " model vdw 1.634 2.450 nonbonded pdb="HE21 GLN I 36 " pdb=" O HOH I 404 " model vdw 1.638 2.450 nonbonded pdb="HE21 GLN E 36 " pdb=" O HOH E 407 " model vdw 1.643 2.450 ... (remaining 469182 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 max=1.00 mean=0.97 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: 9.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.310 Extract box with map and model: 0.700 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 39.370 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:7.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 : 0.003 0.031 14568 Z= 0.146 Angle : 0.537 4.482 20100 Z= 0.330 Chirality : 0.037 0.126 2520 Planarity : 0.003 0.026 2604 Dihedral : 11.387 60.721 5124 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.16), residues: 1932 helix: 1.14 (0.12), residues: 1428 sheet: None (None), residues: 0 loop : -0.45 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 70 TYR 0.012 0.002 TYR I 16 PHE 0.008 0.001 PHE K 59 TRP 0.006 0.001 TRP C 160 HIS 0.012 0.003 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00320 (14568) covalent geometry : angle 0.53717 (20100) hydrogen bonds : bond 0.20790 ( 1221) hydrogen bonds : angle 5.55833 ( 3603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.837 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 1.1928 time to fit residues: 103.5994 Evaluate side-chains 73 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN B 39 GLN ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN D 39 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN H 39 GLN ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN J 39 GLN ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.140467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.115405 restraints weight = 47735.694| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 0.55 r_work: 0.2902 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.2681 rms_B_bonded: 2.68 restraints_weight: 0.1250 r_work: 0.2650 rms_B_bonded: 3.43 restraints_weight: 0.0625 r_work: 0.2632 rms_B_bonded: 4.32 restraints_weight: 0.0312 r_work: 0.2628 rms_B_bonded: 4.68 restraints_weight: 0.0156 r_work: 0.2626 rms_B_bonded: 4.93 restraints_weight: 0.0078 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14568 Z= 0.269 Angle : 0.722 5.834 20100 Z= 0.446 Chirality : 0.044 0.138 2520 Planarity : 0.005 0.037 2604 Dihedral : 4.415 19.861 2172 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.43 (0.17), residues: 1932 helix: 2.20 (0.12), residues: 1476 sheet: None (None), residues: 0 loop : -0.36 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 153 TYR 0.019 0.003 TYR C 16 PHE 0.017 0.003 PHE J 59 TRP 0.008 0.002 TRP G 160 HIS 0.014 0.004 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00510 (14568) covalent geometry : angle 0.72201 (20100) hydrogen bonds : bond 0.12491 ( 1221) hydrogen bonds : angle 4.61122 ( 3603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.758 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 1.1227 time to fit residues: 95.5098 Evaluate side-chains 74 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 174 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.141727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.116668 restraints weight = 46856.178| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 0.57 r_work: 0.2931 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2706 rms_B_bonded: 2.62 restraints_weight: 0.1250 r_work: 0.2675 rms_B_bonded: 3.32 restraints_weight: 0.0625 r_work: 0.2654 rms_B_bonded: 4.30 restraints_weight: 0.0312 r_work: 0.2649 rms_B_bonded: 4.71 restraints_weight: 0.0156 r_work: 0.2647 rms_B_bonded: 4.97 restraints_weight: 0.0078 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14568 Z= 0.239 Angle : 0.663 5.219 20100 Z= 0.412 Chirality : 0.042 0.135 2520 Planarity : 0.004 0.026 2604 Dihedral : 4.379 19.944 2172 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.69 (0.17), residues: 1932 helix: 2.33 (0.12), residues: 1488 sheet: None (None), residues: 0 loop : -0.12 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 70 TYR 0.015 0.003 TYR H 16 PHE 0.016 0.002 PHE D 59 TRP 0.008 0.002 TRP L 160 HIS 0.012 0.004 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00431 (14568) covalent geometry : angle 0.66267 (20100) hydrogen bonds : bond 0.11649 ( 1221) hydrogen bonds : angle 4.51805 ( 3603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.862 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 1.1874 time to fit residues: 102.0476 Evaluate side-chains 72 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.141318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.116129 restraints weight = 47865.347| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 0.57 r_work: 0.2916 rms_B_bonded: 0.95 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 1.45 restraints_weight: 0.2500 r_work: 0.2696 rms_B_bonded: 2.64 restraints_weight: 0.1250 r_work: 0.2667 rms_B_bonded: 3.34 restraints_weight: 0.0625 r_work: 0.2646 rms_B_bonded: 4.33 restraints_weight: 0.0312 r_work: 0.2642 rms_B_bonded: 4.68 restraints_weight: 0.0156 r_work: 0.2640 rms_B_bonded: 4.97 restraints_weight: 0.0078 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14568 Z= 0.246 Angle : 0.676 5.351 20100 Z= 0.419 Chirality : 0.042 0.137 2520 Planarity : 0.004 0.028 2604 Dihedral : 4.425 19.947 2172 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.71 (0.17), residues: 1932 helix: 2.37 (0.12), residues: 1476 sheet: None (None), residues: 0 loop : -0.12 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 70 TYR 0.016 0.003 TYR H 16 PHE 0.016 0.002 PHE B 59 TRP 0.006 0.002 TRP L 160 HIS 0.013 0.004 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00447 (14568) covalent geometry : angle 0.67613 (20100) hydrogen bonds : bond 0.11855 ( 1221) hydrogen bonds : angle 4.52701 ( 3603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.838 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 1.0632 time to fit residues: 90.5167 Evaluate side-chains 71 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 125 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.140551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.115854 restraints weight = 45059.418| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 0.54 r_work: 0.2907 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 1.46 restraints_weight: 0.2500 r_work: 0.2682 rms_B_bonded: 2.68 restraints_weight: 0.1250 r_work: 0.2654 rms_B_bonded: 3.33 restraints_weight: 0.0625 r_work: 0.2633 rms_B_bonded: 4.32 restraints_weight: 0.0312 r_work: 0.2629 rms_B_bonded: 4.69 restraints_weight: 0.0156 r_work: 0.2627 rms_B_bonded: 4.98 restraints_weight: 0.0078 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2586 r_free = 0.2586 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14568 Z= 0.267 Angle : 0.710 6.064 20100 Z= 0.439 Chirality : 0.043 0.138 2520 Planarity : 0.004 0.030 2604 Dihedral : 4.454 19.823 2172 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.66 (0.17), residues: 1932 helix: 2.34 (0.12), residues: 1476 sheet: None (None), residues: 0 loop : -0.18 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 70 TYR 0.016 0.003 TYR H 16 PHE 0.016 0.002 PHE B 59 TRP 0.007 0.002 TRP G 160 HIS 0.015 0.004 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00505 (14568) covalent geometry : angle 0.71029 (20100) hydrogen bonds : bond 0.12346 ( 1221) hydrogen bonds : angle 4.55948 ( 3603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.823 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 1.1028 time to fit residues: 92.4412 Evaluate side-chains 71 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 16 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.141510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.116507 restraints weight = 45476.369| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 0.55 r_work: 0.2929 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2701 rms_B_bonded: 2.60 restraints_weight: 0.1250 r_work: 0.2670 rms_B_bonded: 3.32 restraints_weight: 0.0625 r_work: 0.2648 rms_B_bonded: 4.31 restraints_weight: 0.0312 r_work: 0.2643 rms_B_bonded: 4.70 restraints_weight: 0.0156 r_work: 0.2641 rms_B_bonded: 5.00 restraints_weight: 0.0078 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14568 Z= 0.243 Angle : 0.670 5.189 20100 Z= 0.415 Chirality : 0.042 0.139 2520 Planarity : 0.004 0.028 2604 Dihedral : 4.449 19.807 2172 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.74 (0.17), residues: 1932 helix: 2.39 (0.12), residues: 1476 sheet: None (None), residues: 0 loop : -0.12 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 70 TYR 0.014 0.003 TYR H 16 PHE 0.015 0.002 PHE D 59 TRP 0.006 0.002 TRP L 160 HIS 0.012 0.004 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00440 (14568) covalent geometry : angle 0.66982 (20100) hydrogen bonds : bond 0.11811 ( 1221) hydrogen bonds : angle 4.51220 ( 3603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.751 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 1.0866 time to fit residues: 90.7411 Evaluate side-chains 72 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 79 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.144889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.121826 restraints weight = 44883.972| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 0.53 r_work: 0.2995 rms_B_bonded: 0.88 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work: 0.2768 rms_B_bonded: 2.62 restraints_weight: 0.1250 r_work: 0.2739 rms_B_bonded: 3.29 restraints_weight: 0.0625 r_work: 0.2714 rms_B_bonded: 4.44 restraints_weight: 0.0312 r_work: 0.2710 rms_B_bonded: 4.79 restraints_weight: 0.0156 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14568 Z= 0.202 Angle : 0.584 4.715 20100 Z= 0.363 Chirality : 0.039 0.130 2520 Planarity : 0.003 0.018 2604 Dihedral : 4.277 19.814 2172 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.86 (0.17), residues: 1932 helix: 2.42 (0.12), residues: 1500 sheet: None (None), residues: 0 loop : -0.01 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 70 TYR 0.011 0.002 TYR H 16 PHE 0.014 0.001 PHE K 59 TRP 0.008 0.001 TRP L 160 HIS 0.010 0.003 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00332 (14568) covalent geometry : angle 0.58447 (20100) hydrogen bonds : bond 0.10438 ( 1221) hydrogen bonds : angle 4.41239 ( 3603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.811 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 1.0592 time to fit residues: 88.3118 Evaluate side-chains 70 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.140551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.115505 restraints weight = 45701.650| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 0.55 r_work: 0.2909 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2682 rms_B_bonded: 2.63 restraints_weight: 0.1250 r_work: 0.2652 rms_B_bonded: 3.30 restraints_weight: 0.0625 r_work: 0.2630 rms_B_bonded: 4.30 restraints_weight: 0.0312 r_work: 0.2626 rms_B_bonded: 4.70 restraints_weight: 0.0156 r_work: 0.2624 rms_B_bonded: 4.95 restraints_weight: 0.0078 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14568 Z= 0.273 Angle : 0.717 6.010 20100 Z= 0.443 Chirality : 0.044 0.141 2520 Planarity : 0.004 0.030 2604 Dihedral : 4.464 19.789 2172 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.70 (0.17), residues: 1932 helix: 2.36 (0.12), residues: 1476 sheet: None (None), residues: 0 loop : -0.11 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 70 TYR 0.017 0.003 TYR H 16 PHE 0.016 0.003 PHE D 59 TRP 0.008 0.002 TRP G 160 HIS 0.015 0.004 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00516 (14568) covalent geometry : angle 0.71727 (20100) hydrogen bonds : bond 0.12499 ( 1221) hydrogen bonds : angle 4.55988 ( 3603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.835 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 1.0614 time to fit residues: 88.8147 Evaluate side-chains 72 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.142792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.117827 restraints weight = 45360.287| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 0.55 r_work: 0.2961 rms_B_bonded: 0.86 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 1.35 restraints_weight: 0.2500 r_work: 0.2727 rms_B_bonded: 2.53 restraints_weight: 0.1250 r_work: 0.2692 rms_B_bonded: 3.28 restraints_weight: 0.0625 r_work: 0.2667 rms_B_bonded: 4.37 restraints_weight: 0.0312 r_work: 0.2663 rms_B_bonded: 4.75 restraints_weight: 0.0156 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14568 Z= 0.224 Angle : 0.635 4.977 20100 Z= 0.394 Chirality : 0.041 0.135 2520 Planarity : 0.004 0.024 2604 Dihedral : 4.388 19.739 2172 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.73 (0.17), residues: 1932 helix: 2.35 (0.12), residues: 1500 sheet: None (None), residues: 0 loop : -0.12 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 70 TYR 0.013 0.002 TYR H 16 PHE 0.015 0.002 PHE D 59 TRP 0.008 0.002 TRP L 160 HIS 0.011 0.003 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00391 (14568) covalent geometry : angle 0.63458 (20100) hydrogen bonds : bond 0.11220 ( 1221) hydrogen bonds : angle 4.47139 ( 3603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.817 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 1.1227 time to fit residues: 93.1342 Evaluate side-chains 72 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.143972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.119579 restraints weight = 44217.475| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 0.54 r_work: 0.2990 rms_B_bonded: 0.83 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 1.32 restraints_weight: 0.2500 r_work: 0.2748 rms_B_bonded: 2.51 restraints_weight: 0.1250 r_work: 0.2709 rms_B_bonded: 3.37 restraints_weight: 0.0625 r_work: 0.2686 rms_B_bonded: 4.40 restraints_weight: 0.0312 r_work: 0.2682 rms_B_bonded: 4.75 restraints_weight: 0.0156 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14568 Z= 0.210 Angle : 0.606 4.821 20100 Z= 0.376 Chirality : 0.040 0.132 2520 Planarity : 0.003 0.022 2604 Dihedral : 4.339 19.825 2172 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.81 (0.17), residues: 1932 helix: 2.40 (0.12), residues: 1500 sheet: None (None), residues: 0 loop : -0.05 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 70 TYR 0.011 0.002 TYR K 16 PHE 0.014 0.001 PHE D 59 TRP 0.008 0.001 TRP L 160 HIS 0.010 0.003 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00354 (14568) covalent geometry : angle 0.60578 (20100) hydrogen bonds : bond 0.10770 ( 1221) hydrogen bonds : angle 4.43552 ( 3603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue SER 24 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LEU 92 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 105 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 134 is missing expected H atoms. Skipping. Residue LYS 140 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.704 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 1.0941 time to fit residues: 90.8777 Evaluate side-chains 72 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 12 optimal weight: 0.0050 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.143823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.120772 restraints weight = 46082.840| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 0.52 r_work: 0.2975 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2749 rms_B_bonded: 2.60 restraints_weight: 0.1250 r_work: 0.2719 rms_B_bonded: 3.30 restraints_weight: 0.0625 r_work: 0.2696 rms_B_bonded: 4.36 restraints_weight: 0.0312 r_work: 0.2691 rms_B_bonded: 4.76 restraints_weight: 0.0156 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14568 Z= 0.211 Angle : 0.608 4.853 20100 Z= 0.377 Chirality : 0.040 0.132 2520 Planarity : 0.003 0.022 2604 Dihedral : 4.332 19.803 2172 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.78 (0.17), residues: 1932 helix: 2.37 (0.12), residues: 1500 sheet: None (None), residues: 0 loop : -0.04 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 70 TYR 0.011 0.002 TYR H 16 PHE 0.014 0.001 PHE D 59 TRP 0.008 0.001 TRP L 160 HIS 0.010 0.003 HIS B 51 Details of bonding type rmsd covalent geometry : bond 0.00356 (14568) covalent geometry : angle 0.60814 (20100) hydrogen bonds : bond 0.10810 ( 1221) hydrogen bonds : angle 4.44271 ( 3603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31788.17 seconds wall clock time: 535 minutes 41.58 seconds (32141.58 seconds total)