Starting phenix.real_space_refine on Sun Jul 5 15:53:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zc2_74020/07_2026/9zc2_74020.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zc2_74020/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9zc2_74020/07_2026/9zc2_74020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zc2_74020/07_2026/9zc2_74020.map" model { file = "/net/cci-nas-00/data/ceres_data/9zc2_74020/07_2026/9zc2_74020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zc2_74020/07_2026/9zc2_74020.cif" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' FE': 1} Chain breaks: 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: 9.92, per 1000 atoms: 0.34 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: 2.48 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: 0.55 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: 7.78 Time building geometry restraints manager: 3.47 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: 0.08 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: 9.820 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: 0.240 Extract box with map and model: 0.590 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 35.230 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 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/Z covalent geometry : bond 0.00320 / 0.15 (14568) covalent geometry : angle 0.53717 / 0.33 (20100) hydrogen bonds : bond 0.20790 / 14.16 ( 1221) hydrogen bonds : angle 5.55833 / 4.11 ( 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 : 0.658 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.9461 time to fit residues: 83.0623 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 : 0.782 ------------------------------------------------------------------------------- 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... 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 = 0.3465 r_free = 0.3465 target = 0.141234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.116035 restraints weight = 46821.134| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 0.55 r_work: 0.2909 rms_B_bonded: 0.96 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 1.47 restraints_weight: 0.2500 r_work: 0.2689 rms_B_bonded: 2.69 restraints_weight: 0.1250 r_work: 0.2655 rms_B_bonded: 3.61 restraints_weight: 0.0625 r_work: 0.2641 rms_B_bonded: 4.36 restraints_weight: 0.0312 r_work: 0.2637 rms_B_bonded: 4.72 restraints_weight: 0.0156 r_work: 0.2636 rms_B_bonded: 4.93 restraints_weight: 0.0078 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 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 = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0893 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= 0.270 Angle : 0.726 6.625 20100 Z= 0.447 Chirality : 0.044 0.136 2520 Planarity : 0.005 0.037 2604 Dihedral : 4.413 19.814 2172 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.99 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: 2.44 (0.17), residues: 1932 helix: 2.21 (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 0.013 0.004 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.27 (14568) covalent geometry : angle 0.72632 / 0.45 (20100) hydrogen bonds : bond 0.12497 / 8.50 ( 1221) hydrogen bonds : angle 4.61604 / 3.42 ( 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 : 0.938 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.9604 time to fit residues: 82.3354 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 : 0.582 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3478 r_free = 0.3478 target = 0.142345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.117424 restraints weight = 44900.328| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 0.52 r_work: 0.2943 rms_B_bonded: 0.89 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2711 rms_B_bonded: 2.60 restraints_weight: 0.1250 r_work: 0.2676 rms_B_bonded: 3.43 restraints_weight: 0.0625 r_work: 0.2657 rms_B_bonded: 4.35 restraints_weight: 0.0312 r_work: 0.2653 rms_B_bonded: 4.68 restraints_weight: 0.0156 r_work: 0.2651 rms_B_bonded: 4.99 restraints_weight: 0.0078 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14568 Z= 0.248 Angle : 0.681 5.757 20100 Z= 0.422 Chirality : 0.042 0.136 2520 Planarity : 0.004 0.028 2604 Dihedral : 4.405 19.829 2172 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: 2.67 (0.17), residues: 1932 helix: 2.33 (0.12), residues: 1488 sheet: None (None), residues: 0 loop : -0.16 (0.24), residues: 444 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 0.007 0.002 TRP L 160 HIS 0.012 0.004 HIS H 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.25 (14568) covalent geometry : angle 0.68144 / 0.42 (20100) hydrogen bonds : bond 0.11850 / 8.05 ( 1221) hydrogen bonds : angle 4.53911 / 3.37 ( 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 77 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.892 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.9856 time to fit residues: 87.1344 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 : 0.705 ------------------------------------------------------------------------------- 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: 3.9990 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 170 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3475 r_free = 0.3475 target = 0.142063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.116939 restraints weight = 46162.747| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 0.54 r_work: 0.2934 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2704 rms_B_bonded: 2.62 restraints_weight: 0.1250 r_work: 0.2673 rms_B_bonded: 3.36 restraints_weight: 0.0625 r_work: 0.2651 rms_B_bonded: 4.35 restraints_weight: 0.0312 r_work: 0.2648 rms_B_bonded: 4.69 restraints_weight: 0.0156 r_work: 0.2646 rms_B_bonded: 4.97 restraints_weight: 0.0078 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14568 Z= 0.253 Angle : 0.688 5.772 20100 Z= 0.425 Chirality : 0.043 0.138 2520 Planarity : 0.004 0.029 2604 Dihedral : 4.440 19.890 2172 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % 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: 2.31 (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 0.006 0.001 ARG J 70 TYR 0.016 0.003 TYR I 16 PHE 0.016 0.002 PHE B 59 TRP 0.006 0.002 TRP L 160 HIS 0.013 0.004 HIS H 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.25 (14568) covalent geometry : angle 0.68794 / 0.42 (20100) hydrogen bonds : bond 0.11982 / 8.15 ( 1221) hydrogen bonds : angle 4.54088 / 3.37 ( 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 75 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.773 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.9703 time to fit residues: 83.5923 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 : 0.783 ------------------------------------------------------------------------------- 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: 2.9990 chunk 118 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.141342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.116374 restraints weight = 44281.431| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 0.53 r_work: 0.2924 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2695 rms_B_bonded: 2.60 restraints_weight: 0.1250 r_work: 0.2662 rms_B_bonded: 3.36 restraints_weight: 0.0625 r_work: 0.2643 rms_B_bonded: 4.24 restraints_weight: 0.0312 r_work: 0.2638 rms_B_bonded: 4.65 restraints_weight: 0.0156 r_work: 0.2636 rms_B_bonded: 4.93 restraints_weight: 0.0078 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14568 Z= 0.268 Angle : 0.715 7.091 20100 Z= 0.441 Chirality : 0.044 0.139 2520 Planarity : 0.004 0.030 2604 Dihedral : 4.460 19.812 2172 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % 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: 2.68 (0.17), residues: 1932 helix: 2.36 (0.12), residues: 1476 sheet: None (None), residues: 0 loop : -0.20 (0.23), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 70 TYR 0.017 0.003 TYR H 16 PHE 0.016 0.002 PHE B 59 TRP 0.007 0.002 TRP G 160 HIS 0.013 0.004 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.27 (14568) covalent geometry : angle 0.71523 / 0.44 (20100) hydrogen bonds : bond 0.12330 / 8.38 ( 1221) hydrogen bonds : angle 4.56375 / 3.38 ( 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 74 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.711 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.8912 time to fit residues: 76.0858 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 : 0.743 ------------------------------------------------------------------------------- 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: 0.9990 chunk 156 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 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: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3491 r_free = 0.3491 target = 0.143470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.118404 restraints weight = 43430.926| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 0.51 r_work: 0.2957 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2727 rms_B_bonded: 2.64 restraints_weight: 0.1250 r_work: 0.2698 rms_B_bonded: 3.31 restraints_weight: 0.0625 r_work: 0.2676 rms_B_bonded: 4.34 restraints_weight: 0.0312 r_work: 0.2671 rms_B_bonded: 4.79 restraints_weight: 0.0156 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1014 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= 0.232 Angle : 0.650 5.726 20100 Z= 0.402 Chirality : 0.041 0.136 2520 Planarity : 0.004 0.026 2604 Dihedral : 4.408 19.747 2172 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 2.35 (0.12), residues: 1500 sheet: None (None), residues: 0 loop : -0.22 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 H 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.23 (14568) covalent geometry : angle 0.64976 / 0.40 (20100) hydrogen bonds : bond 0.11457 / 7.79 ( 1221) hydrogen bonds : angle 4.49760 / 3.34 ( 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 79 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.730 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.9883 time to fit residues: 89.2040 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 : 0.658 ------------------------------------------------------------------------------- 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: 2.9990 chunk 157 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3502 r_free = 0.3502 target = 0.144384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.120013 restraints weight = 41091.395| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 0.50 r_work: 0.2984 rms_B_bonded: 0.84 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 1.31 restraints_weight: 0.2500 r_work: 0.2741 rms_B_bonded: 2.52 restraints_weight: 0.1250 r_work: 0.2704 rms_B_bonded: 3.36 restraints_weight: 0.0625 r_work: 0.2681 rms_B_bonded: 4.43 restraints_weight: 0.0312 r_work: 0.2677 rms_B_bonded: 4.77 restraints_weight: 0.0156 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14568 Z= 0.225 Angle : 0.634 5.324 20100 Z= 0.393 Chirality : 0.041 0.138 2520 Planarity : 0.004 0.024 2604 Dihedral : 4.382 19.767 2172 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 2.64 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: 2.75 (0.17), residues: 1932 helix: 2.36 (0.12), residues: 1500 sheet: None (None), residues: 0 loop : -0.13 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 70 TYR 0.012 0.002 TYR H 16 PHE 0.015 0.002 PHE D 59 TRP 0.007 0.002 TRP L 160 HIS 0.011 0.003 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.22 (14568) covalent geometry : angle 0.63448 / 0.39 (20100) hydrogen bonds : bond 0.11248 / 7.65 ( 1221) hydrogen bonds : angle 4.47526 / 3.32 ( 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 77 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.804 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.9342 time to fit residues: 82.4513 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 : 0.755 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3474 r_free = 0.3474 target = 0.141998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.116884 restraints weight = 44026.873| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 0.53 r_work: 0.2925 rms_B_bonded: 0.93 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 1.42 restraints_weight: 0.2500 r_work: 0.2701 rms_B_bonded: 2.63 restraints_weight: 0.1250 r_work: 0.2672 rms_B_bonded: 3.28 restraints_weight: 0.0625 r_work: 0.2648 rms_B_bonded: 4.37 restraints_weight: 0.0312 r_work: 0.2644 rms_B_bonded: 4.75 restraints_weight: 0.0156 r_work: 0.2643 rms_B_bonded: 4.98 restraints_weight: 0.0078 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14568 Z= 0.262 Angle : 0.704 7.182 20100 Z= 0.434 Chirality : 0.043 0.140 2520 Planarity : 0.004 0.028 2604 Dihedral : 4.453 19.898 2172 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: 2.38 (0.12), residues: 1476 sheet: None (None), residues: 0 loop : -0.10 (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 0.007 0.002 TRP G 160 HIS 0.014 0.004 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.26 (14568) covalent geometry : angle 0.70437 / 0.43 (20100) hydrogen bonds : bond 0.12240 / 8.32 ( 1221) hydrogen bonds : angle 4.54875 / 3.37 ( 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 : 0.823 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.9086 time to fit residues: 76.2640 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 : 0.795 ------------------------------------------------------------------------------- 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: 0.9990 chunk 56 optimal weight: 0.5980 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: 3.9990 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3491 r_free = 0.3491 target = 0.143384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.119054 restraints weight = 42595.516| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 0.51 r_work: 0.2981 rms_B_bonded: 0.79 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 1.27 restraints_weight: 0.2500 r_work: 0.2729 rms_B_bonded: 2.45 restraints_weight: 0.1250 r_work: 0.2688 rms_B_bonded: 3.32 restraints_weight: 0.0625 r_work: 0.2664 rms_B_bonded: 4.40 restraints_weight: 0.0312 r_work: 0.2660 rms_B_bonded: 4.76 restraints_weight: 0.0156 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14568 Z= 0.237 Angle : 0.659 5.849 20100 Z= 0.407 Chirality : 0.042 0.138 2520 Planarity : 0.004 0.027 2604 Dihedral : 4.434 19.740 2172 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: 1500 sheet: None (None), residues: 0 loop : -0.18 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 70 TYR 0.013 0.002 TYR H 16 PHE 0.015 0.002 PHE D 59 TRP 0.007 0.002 TRP L 160 HIS 0.012 0.004 HIS H 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.24 (14568) covalent geometry : angle 0.65913 / 0.41 (20100) hydrogen bonds : bond 0.11626 / 7.90 ( 1221) hydrogen bonds : angle 4.49972 / 3.34 ( 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 72 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.829 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.9385 time to fit residues: 77.7603 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 : 0.586 ------------------------------------------------------------------------------- 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: 5.9990 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: 3.9990 chunk 163 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 138 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3556 r_free = 0.3556 target = 0.148955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.124481 restraints weight = 38406.261| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 0.44 r_work: 0.3056 rms_B_bonded: 0.80 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 1.28 restraints_weight: 0.2500 r_work: 0.2815 rms_B_bonded: 2.49 restraints_weight: 0.1250 r_work: 0.2778 rms_B_bonded: 3.34 restraints_weight: 0.0625 r_work: 0.2754 rms_B_bonded: 4.46 restraints_weight: 0.0312 r_work: 0.2749 rms_B_bonded: 4.88 restraints_weight: 0.0156 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14568 Z= 0.194 Angle : 0.577 4.654 20100 Z= 0.357 Chirality : 0.039 0.130 2520 Planarity : 0.003 0.019 2604 Dihedral : 4.274 19.548 2172 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: 2.91 (0.17), residues: 1932 helix: 2.46 (0.12), residues: 1500 sheet: None (None), residues: 0 loop : 0.00 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 124 TYR 0.010 0.002 TYR H 16 PHE 0.014 0.001 PHE K 59 TRP 0.009 0.001 TRP L 160 HIS 0.008 0.002 HIS B 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.19 (14568) covalent geometry : angle 0.57676 / 0.36 (20100) hydrogen bonds : bond 0.10112 / 6.88 ( 1221) hydrogen bonds : angle 4.40280 / 3.28 ( 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 78 residues out of total 1500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 1.0648 time to fit residues: 94.3427 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 : 0.802 ------------------------------------------------------------------------------- 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: 2.9990 chunk 125 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3500 r_free = 0.3500 target = 0.144243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.119541 restraints weight = 41697.051| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 0.51 r_work: 0.2963 rms_B_bonded: 0.89 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 1.40 restraints_weight: 0.2500 r_work: 0.2735 rms_B_bonded: 2.59 restraints_weight: 0.1250 r_work: 0.2705 rms_B_bonded: 3.27 restraints_weight: 0.0625 r_work: 0.2681 rms_B_bonded: 4.32 restraints_weight: 0.0312 r_work: 0.2676 rms_B_bonded: 4.74 restraints_weight: 0.0156 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14568 Z= 0.233 Angle : 0.650 6.096 20100 Z= 0.402 Chirality : 0.042 0.137 2520 Planarity : 0.004 0.024 2604 Dihedral : 4.374 19.807 2172 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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: 2.75 (0.17), residues: 1932 helix: 2.36 (0.12), residues: 1500 sheet: None (None), residues: 0 loop : -0.08 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 70 TYR 0.013 0.002 TYR H 16 PHE 0.015 0.002 PHE D 59 TRP 0.006 0.002 TRP L 160 HIS 0.012 0.003 HIS D 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.23 (14568) covalent geometry : angle 0.65042 / 0.40 (20100) hydrogen bonds : bond 0.11497 / 7.82 ( 1221) hydrogen bonds : angle 4.48509 / 3.33 ( 3603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29122.81 seconds wall clock time: 490 minutes 10.34 seconds (29410.34 seconds total)