Starting phenix.real_space_refine on Sat Mar 7 14:04:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cw4_27023/03_2026/8cw4_27023_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cw4_27023/03_2026/8cw4_27023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cw4_27023/03_2026/8cw4_27023_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cw4_27023/03_2026/8cw4_27023_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cw4_27023/03_2026/8cw4_27023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cw4_27023/03_2026/8cw4_27023.map" } resolution = 3.0 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= 0.006 sd= 0.094 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 70 5.49 5 S 350 5.16 5 C 26110 2.51 5 N 5530 2.21 5 O 7210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39270 Number of models: 1 Model: "" Number of chains: 135 Chain: "1A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.01, per 1000 atoms: 0.20 Number of scatterers: 39270 At special positions: 0 Unit cell: (92.65, 92.65, 262.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 350 16.00 P 70 15.00 O 7210 8.00 N 5530 7.00 C 26110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.3 seconds 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8820 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 0 sheets defined 81.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain '1A' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1A 46 " --> pdb=" O THR1A 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP1A 47 " --> pdb=" O TRP1A 43 " (cutoff:3.500A) Proline residue: 1A 49 - end of helix Processing helix chain '1A' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG1A 75 " --> pdb=" O SER1A 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1A 77 " --> pdb=" O ILE1A 73 " (cutoff:3.500A) Processing helix chain '1A' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR1A 93 " --> pdb=" O LEU1A 89 " (cutoff:3.500A) Processing helix chain '1B' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1B 46 " --> pdb=" O THR1B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1B 47 " --> pdb=" O TRP1B 43 " (cutoff:3.500A) Proline residue: 1B 49 - end of helix Processing helix chain '1B' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG1B 75 " --> pdb=" O SER1B 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1B 77 " --> pdb=" O ILE1B 73 " (cutoff:3.500A) Processing helix chain '1B' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR1B 93 " --> pdb=" O LEU1B 89 " (cutoff:3.500A) Processing helix chain '1C' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR1C 46 " --> pdb=" O THR1C 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1C 47 " --> pdb=" O TRP1C 43 " (cutoff:3.500A) Proline residue: 1C 49 - end of helix Processing helix chain '1C' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1C 75 " --> pdb=" O SER1C 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1C 77 " --> pdb=" O ILE1C 73 " (cutoff:3.500A) Processing helix chain '1C' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR1C 93 " --> pdb=" O LEU1C 89 " (cutoff:3.500A) Processing helix chain '1D' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1D 46 " --> pdb=" O THR1D 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1D 47 " --> pdb=" O TRP1D 43 " (cutoff:3.500A) Proline residue: 1D 49 - end of helix Processing helix chain '1D' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1D 75 " --> pdb=" O SER1D 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL1D 77 " --> pdb=" O ILE1D 73 " (cutoff:3.500A) Processing helix chain '1D' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR1D 93 " --> pdb=" O LEU1D 89 " (cutoff:3.500A) Processing helix chain '1E' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1E 46 " --> pdb=" O THR1E 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1E 47 " --> pdb=" O TRP1E 43 " (cutoff:3.500A) Proline residue: 1E 49 - end of helix Processing helix chain '1E' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1E 75 " --> pdb=" O SER1E 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1E 77 " --> pdb=" O ILE1E 73 " (cutoff:3.500A) Processing helix chain '1E' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR1E 93 " --> pdb=" O LEU1E 89 " (cutoff:3.500A) Processing helix chain '1F' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1F 46 " --> pdb=" O THR1F 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1F 47 " --> pdb=" O TRP1F 43 " (cutoff:3.500A) Proline residue: 1F 49 - end of helix Processing helix chain '1F' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1F 75 " --> pdb=" O SER1F 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1F 77 " --> pdb=" O ILE1F 73 " (cutoff:3.500A) Processing helix chain '1F' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR1F 93 " --> pdb=" O LEU1F 89 " (cutoff:3.500A) Processing helix chain '1G' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1G 46 " --> pdb=" O THR1G 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1G 47 " --> pdb=" O TRP1G 43 " (cutoff:3.500A) Proline residue: 1G 49 - end of helix Processing helix chain '1G' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1G 75 " --> pdb=" O SER1G 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1G 77 " --> pdb=" O ILE1G 73 " (cutoff:3.500A) Processing helix chain '1G' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR1G 93 " --> pdb=" O LEU1G 89 " (cutoff:3.500A) Processing helix chain '1H' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1H 46 " --> pdb=" O THR1H 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP1H 47 " --> pdb=" O TRP1H 43 " (cutoff:3.500A) Proline residue: 1H 49 - end of helix Processing helix chain '1H' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG1H 75 " --> pdb=" O SER1H 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL1H 77 " --> pdb=" O ILE1H 73 " (cutoff:3.500A) Processing helix chain '1H' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR1H 93 " --> pdb=" O LEU1H 89 " (cutoff:3.500A) Processing helix chain '1I' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1I 46 " --> pdb=" O THR1I 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1I 47 " --> pdb=" O TRP1I 43 " (cutoff:3.500A) Proline residue: 1I 49 - end of helix Processing helix chain '1I' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1I 75 " --> pdb=" O SER1I 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL1I 77 " --> pdb=" O ILE1I 73 " (cutoff:3.500A) Processing helix chain '1I' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR1I 93 " --> pdb=" O LEU1I 89 " (cutoff:3.500A) Processing helix chain '1J' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1J 46 " --> pdb=" O THR1J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1J 47 " --> pdb=" O TRP1J 43 " (cutoff:3.500A) Proline residue: 1J 49 - end of helix Processing helix chain '1J' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1J 75 " --> pdb=" O SER1J 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1J 77 " --> pdb=" O ILE1J 73 " (cutoff:3.500A) Processing helix chain '1J' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR1J 93 " --> pdb=" O LEU1J 89 " (cutoff:3.500A) Processing helix chain '1K' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR1K 46 " --> pdb=" O THR1K 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1K 47 " --> pdb=" O TRP1K 43 " (cutoff:3.500A) Proline residue: 1K 49 - end of helix Processing helix chain '1K' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1K 75 " --> pdb=" O SER1K 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1K 77 " --> pdb=" O ILE1K 73 " (cutoff:3.500A) Processing helix chain '1K' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR1K 93 " --> pdb=" O LEU1K 89 " (cutoff:3.500A) Processing helix chain '1L' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1L 46 " --> pdb=" O THR1L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1L 47 " --> pdb=" O TRP1L 43 " (cutoff:3.500A) Proline residue: 1L 49 - end of helix Processing helix chain '1L' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1L 75 " --> pdb=" O SER1L 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL1L 77 " --> pdb=" O ILE1L 73 " (cutoff:3.500A) Processing helix chain '1L' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR1L 93 " --> pdb=" O LEU1L 89 " (cutoff:3.500A) Processing helix chain '1M' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1M 46 " --> pdb=" O THR1M 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP1M 47 " --> pdb=" O TRP1M 43 " (cutoff:3.500A) Proline residue: 1M 49 - end of helix Processing helix chain '1M' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG1M 75 " --> pdb=" O SER1M 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1M 77 " --> pdb=" O ILE1M 73 " (cutoff:3.500A) Processing helix chain '1M' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR1M 93 " --> pdb=" O LEU1M 89 " (cutoff:3.500A) Processing helix chain '1N' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR1N 46 " --> pdb=" O THR1N 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP1N 47 " --> pdb=" O TRP1N 43 " (cutoff:3.500A) Proline residue: 1N 49 - end of helix Processing helix chain '1N' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG1N 75 " --> pdb=" O SER1N 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL1N 77 " --> pdb=" O ILE1N 73 " (cutoff:3.500A) Processing helix chain '1N' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR1N 93 " --> pdb=" O LEU1N 89 " (cutoff:3.500A) Processing helix chain '2A' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2A 46 " --> pdb=" O THR2A 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2A 47 " --> pdb=" O TRP2A 43 " (cutoff:3.500A) Proline residue: 2A 49 - end of helix Processing helix chain '2A' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG2A 75 " --> pdb=" O SER2A 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2A 77 " --> pdb=" O ILE2A 73 " (cutoff:3.500A) Processing helix chain '2A' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR2A 93 " --> pdb=" O LEU2A 89 " (cutoff:3.500A) Processing helix chain '2B' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2B 46 " --> pdb=" O THR2B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2B 47 " --> pdb=" O TRP2B 43 " (cutoff:3.500A) Proline residue: 2B 49 - end of helix Processing helix chain '2B' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG2B 75 " --> pdb=" O SER2B 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2B 77 " --> pdb=" O ILE2B 73 " (cutoff:3.500A) Processing helix chain '2B' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR2B 93 " --> pdb=" O LEU2B 89 " (cutoff:3.500A) Processing helix chain '2C' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2C 46 " --> pdb=" O THR2C 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2C 47 " --> pdb=" O TRP2C 43 " (cutoff:3.500A) Proline residue: 2C 49 - end of helix Processing helix chain '2C' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG2C 75 " --> pdb=" O SER2C 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL2C 77 " --> pdb=" O ILE2C 73 " (cutoff:3.500A) Processing helix chain '2C' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR2C 93 " --> pdb=" O LEU2C 89 " (cutoff:3.500A) Processing helix chain '2D' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2D 46 " --> pdb=" O THR2D 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2D 47 " --> pdb=" O TRP2D 43 " (cutoff:3.500A) Proline residue: 2D 49 - end of helix Processing helix chain '2D' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG2D 75 " --> pdb=" O SER2D 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2D 77 " --> pdb=" O ILE2D 73 " (cutoff:3.500A) Processing helix chain '2D' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR2D 93 " --> pdb=" O LEU2D 89 " (cutoff:3.500A) Processing helix chain '2E' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2E 46 " --> pdb=" O THR2E 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP2E 47 " --> pdb=" O TRP2E 43 " (cutoff:3.500A) Proline residue: 2E 49 - end of helix Processing helix chain '2E' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG2E 75 " --> pdb=" O SER2E 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2E 77 " --> pdb=" O ILE2E 73 " (cutoff:3.500A) Processing helix chain '2E' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR2E 93 " --> pdb=" O LEU2E 89 " (cutoff:3.500A) Processing helix chain '2F' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2F 46 " --> pdb=" O THR2F 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2F 47 " --> pdb=" O TRP2F 43 " (cutoff:3.500A) Proline residue: 2F 49 - end of helix Processing helix chain '2F' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG2F 75 " --> pdb=" O SER2F 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2F 77 " --> pdb=" O ILE2F 73 " (cutoff:3.500A) Processing helix chain '2F' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR2F 93 " --> pdb=" O LEU2F 89 " (cutoff:3.500A) Processing helix chain '2G' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2G 46 " --> pdb=" O THR2G 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2G 47 " --> pdb=" O TRP2G 43 " (cutoff:3.500A) Proline residue: 2G 49 - end of helix Processing helix chain '2G' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG2G 75 " --> pdb=" O SER2G 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL2G 77 " --> pdb=" O ILE2G 73 " (cutoff:3.500A) Processing helix chain '2G' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR2G 93 " --> pdb=" O LEU2G 89 " (cutoff:3.500A) Processing helix chain '2H' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR2H 46 " --> pdb=" O THR2H 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2H 47 " --> pdb=" O TRP2H 43 " (cutoff:3.500A) Proline residue: 2H 49 - end of helix Processing helix chain '2H' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG2H 75 " --> pdb=" O SER2H 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL2H 77 " --> pdb=" O ILE2H 73 " (cutoff:3.500A) Processing helix chain '2H' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR2H 93 " --> pdb=" O LEU2H 89 " (cutoff:3.500A) Processing helix chain '2I' and resid 33 through 65 removed outlier: 3.646A pdb=" N THR2I 46 " --> pdb=" O THR2I 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2I 47 " --> pdb=" O TRP2I 43 " (cutoff:3.500A) Proline residue: 2I 49 - end of helix Processing helix chain '2I' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG2I 75 " --> pdb=" O SER2I 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2I 77 " --> pdb=" O ILE2I 73 " (cutoff:3.500A) Processing helix chain '2I' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR2I 93 " --> pdb=" O LEU2I 89 " (cutoff:3.500A) Processing helix chain '2J' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2J 46 " --> pdb=" O THR2J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2J 47 " --> pdb=" O TRP2J 43 " (cutoff:3.500A) Proline residue: 2J 49 - end of helix Processing helix chain '2J' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG2J 75 " --> pdb=" O SER2J 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL2J 77 " --> pdb=" O ILE2J 73 " (cutoff:3.500A) Processing helix chain '2J' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR2J 93 " --> pdb=" O LEU2J 89 " (cutoff:3.500A) Processing helix chain '2K' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2K 46 " --> pdb=" O THR2K 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2K 47 " --> pdb=" O TRP2K 43 " (cutoff:3.500A) Proline residue: 2K 49 - end of helix Processing helix chain '2K' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG2K 75 " --> pdb=" O SER2K 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2K 77 " --> pdb=" O ILE2K 73 " (cutoff:3.500A) Processing helix chain '2K' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR2K 93 " --> pdb=" O LEU2K 89 " (cutoff:3.500A) Processing helix chain '2L' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2L 46 " --> pdb=" O THR2L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2L 47 " --> pdb=" O TRP2L 43 " (cutoff:3.500A) Proline residue: 2L 49 - end of helix Processing helix chain '2L' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG2L 75 " --> pdb=" O SER2L 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2L 77 " --> pdb=" O ILE2L 73 " (cutoff:3.500A) Processing helix chain '2L' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR2L 93 " --> pdb=" O LEU2L 89 " (cutoff:3.500A) Processing helix chain '2M' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2M 46 " --> pdb=" O THR2M 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2M 47 " --> pdb=" O TRP2M 43 " (cutoff:3.500A) Proline residue: 2M 49 - end of helix Processing helix chain '2M' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG2M 75 " --> pdb=" O SER2M 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2M 77 " --> pdb=" O ILE2M 73 " (cutoff:3.500A) Processing helix chain '2M' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR2M 93 " --> pdb=" O LEU2M 89 " (cutoff:3.500A) Processing helix chain '2N' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR2N 46 " --> pdb=" O THR2N 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2N 47 " --> pdb=" O TRP2N 43 " (cutoff:3.500A) Proline residue: 2N 49 - end of helix Processing helix chain '2N' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG2N 75 " --> pdb=" O SER2N 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL2N 77 " --> pdb=" O ILE2N 73 " (cutoff:3.500A) Processing helix chain '2N' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR2N 93 " --> pdb=" O LEU2N 89 " (cutoff:3.500A) Processing helix chain '3A' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3A 46 " --> pdb=" O THR3A 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3A 47 " --> pdb=" O TRP3A 43 " (cutoff:3.500A) Proline residue: 3A 49 - end of helix Processing helix chain '3A' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG3A 75 " --> pdb=" O SER3A 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3A 77 " --> pdb=" O ILE3A 73 " (cutoff:3.500A) Processing helix chain '3A' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR3A 93 " --> pdb=" O LEU3A 89 " (cutoff:3.500A) Processing helix chain '3B' and resid 33 through 65 removed outlier: 3.646A pdb=" N THR3B 46 " --> pdb=" O THR3B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3B 47 " --> pdb=" O TRP3B 43 " (cutoff:3.500A) Proline residue: 3B 49 - end of helix Processing helix chain '3B' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG3B 75 " --> pdb=" O SER3B 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3B 77 " --> pdb=" O ILE3B 73 " (cutoff:3.500A) Processing helix chain '3B' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR3B 93 " --> pdb=" O LEU3B 89 " (cutoff:3.500A) Processing helix chain '3C' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3C 46 " --> pdb=" O THR3C 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP3C 47 " --> pdb=" O TRP3C 43 " (cutoff:3.500A) Proline residue: 3C 49 - end of helix Processing helix chain '3C' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG3C 75 " --> pdb=" O SER3C 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3C 77 " --> pdb=" O ILE3C 73 " (cutoff:3.500A) Processing helix chain '3C' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR3C 93 " --> pdb=" O LEU3C 89 " (cutoff:3.500A) Processing helix chain '3D' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3D 46 " --> pdb=" O THR3D 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3D 47 " --> pdb=" O TRP3D 43 " (cutoff:3.500A) Proline residue: 3D 49 - end of helix Processing helix chain '3D' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG3D 75 " --> pdb=" O SER3D 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL3D 77 " --> pdb=" O ILE3D 73 " (cutoff:3.500A) Processing helix chain '3D' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR3D 93 " --> pdb=" O LEU3D 89 " (cutoff:3.500A) Processing helix chain '3E' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3E 46 " --> pdb=" O THR3E 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3E 47 " --> pdb=" O TRP3E 43 " (cutoff:3.500A) Proline residue: 3E 49 - end of helix Processing helix chain '3E' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG3E 75 " --> pdb=" O SER3E 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3E 77 " --> pdb=" O ILE3E 73 " (cutoff:3.500A) Processing helix chain '3E' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR3E 93 " --> pdb=" O LEU3E 89 " (cutoff:3.500A) Processing helix chain '3F' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR3F 46 " --> pdb=" O THR3F 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP3F 47 " --> pdb=" O TRP3F 43 " (cutoff:3.500A) Proline residue: 3F 49 - end of helix Processing helix chain '3F' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG3F 75 " --> pdb=" O SER3F 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3F 77 " --> pdb=" O ILE3F 73 " (cutoff:3.500A) Processing helix chain '3F' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR3F 93 " --> pdb=" O LEU3F 89 " (cutoff:3.500A) Processing helix chain '3G' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3G 46 " --> pdb=" O THR3G 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP3G 47 " --> pdb=" O TRP3G 43 " (cutoff:3.500A) Proline residue: 3G 49 - end of helix Processing helix chain '3G' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG3G 75 " --> pdb=" O SER3G 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3G 77 " --> pdb=" O ILE3G 73 " (cutoff:3.500A) Processing helix chain '3G' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR3G 93 " --> pdb=" O LEU3G 89 " (cutoff:3.500A) Processing helix chain '3H' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3H 46 " --> pdb=" O THR3H 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3H 47 " --> pdb=" O TRP3H 43 " (cutoff:3.500A) Proline residue: 3H 49 - end of helix Processing helix chain '3H' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG3H 75 " --> pdb=" O SER3H 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3H 77 " --> pdb=" O ILE3H 73 " (cutoff:3.500A) Processing helix chain '3H' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR3H 93 " --> pdb=" O LEU3H 89 " (cutoff:3.500A) Processing helix chain '3I' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3I 46 " --> pdb=" O THR3I 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP3I 47 " --> pdb=" O TRP3I 43 " (cutoff:3.500A) Proline residue: 3I 49 - end of helix Processing helix chain '3I' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG3I 75 " --> pdb=" O SER3I 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL3I 77 " --> pdb=" O ILE3I 73 " (cutoff:3.500A) Processing helix chain '3I' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR3I 93 " --> pdb=" O LEU3I 89 " (cutoff:3.500A) Processing helix chain '3J' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR3J 46 " --> pdb=" O THR3J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3J 47 " --> pdb=" O TRP3J 43 " (cutoff:3.500A) Proline residue: 3J 49 - end of helix Processing helix chain '3J' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG3J 75 " --> pdb=" O SER3J 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3J 77 " --> pdb=" O ILE3J 73 " (cutoff:3.500A) Processing helix chain '3J' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR3J 93 " --> pdb=" O LEU3J 89 " (cutoff:3.500A) Processing helix chain '3K' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3K 46 " --> pdb=" O THR3K 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3K 47 " --> pdb=" O TRP3K 43 " (cutoff:3.500A) Proline residue: 3K 49 - end of helix Processing helix chain '3K' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG3K 75 " --> pdb=" O SER3K 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3K 77 " --> pdb=" O ILE3K 73 " (cutoff:3.500A) Processing helix chain '3K' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR3K 93 " --> pdb=" O LEU3K 89 " (cutoff:3.500A) Processing helix chain '3L' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3L 46 " --> pdb=" O THR3L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3L 47 " --> pdb=" O TRP3L 43 " (cutoff:3.500A) Proline residue: 3L 49 - end of helix Processing helix chain '3L' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG3L 75 " --> pdb=" O SER3L 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3L 77 " --> pdb=" O ILE3L 73 " (cutoff:3.500A) Processing helix chain '3L' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR3L 93 " --> pdb=" O LEU3L 89 " (cutoff:3.500A) Processing helix chain '3M' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR3M 46 " --> pdb=" O THR3M 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3M 47 " --> pdb=" O TRP3M 43 " (cutoff:3.500A) Proline residue: 3M 49 - end of helix Processing helix chain '3M' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG3M 75 " --> pdb=" O SER3M 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3M 77 " --> pdb=" O ILE3M 73 " (cutoff:3.500A) Processing helix chain '3M' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR3M 93 " --> pdb=" O LEU3M 89 " (cutoff:3.500A) Processing helix chain '3N' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR3N 46 " --> pdb=" O THR3N 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3N 47 " --> pdb=" O TRP3N 43 " (cutoff:3.500A) Proline residue: 3N 49 - end of helix Processing helix chain '3N' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG3N 75 " --> pdb=" O SER3N 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL3N 77 " --> pdb=" O ILE3N 73 " (cutoff:3.500A) Processing helix chain '3N' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR3N 93 " --> pdb=" O LEU3N 89 " (cutoff:3.500A) Processing helix chain '4A' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR4A 46 " --> pdb=" O THR4A 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4A 47 " --> pdb=" O TRP4A 43 " (cutoff:3.500A) Proline residue: 4A 49 - end of helix Processing helix chain '4A' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG4A 75 " --> pdb=" O SER4A 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4A 77 " --> pdb=" O ILE4A 73 " (cutoff:3.500A) Processing helix chain '4A' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4A 93 " --> pdb=" O LEU4A 89 " (cutoff:3.500A) Processing helix chain '4B' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4B 46 " --> pdb=" O THR4B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4B 47 " --> pdb=" O TRP4B 43 " (cutoff:3.500A) Proline residue: 4B 49 - end of helix Processing helix chain '4B' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG4B 75 " --> pdb=" O SER4B 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4B 77 " --> pdb=" O ILE4B 73 " (cutoff:3.500A) Processing helix chain '4B' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR4B 93 " --> pdb=" O LEU4B 89 " (cutoff:3.500A) Processing helix chain '4C' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4C 46 " --> pdb=" O THR4C 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4C 47 " --> pdb=" O TRP4C 43 " (cutoff:3.500A) Proline residue: 4C 49 - end of helix Processing helix chain '4C' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG4C 75 " --> pdb=" O SER4C 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4C 77 " --> pdb=" O ILE4C 73 " (cutoff:3.500A) Processing helix chain '4C' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR4C 93 " --> pdb=" O LEU4C 89 " (cutoff:3.500A) Processing helix chain '4D' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4D 46 " --> pdb=" O THR4D 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP4D 47 " --> pdb=" O TRP4D 43 " (cutoff:3.500A) Proline residue: 4D 49 - end of helix Processing helix chain '4D' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG4D 75 " --> pdb=" O SER4D 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4D 77 " --> pdb=" O ILE4D 73 " (cutoff:3.500A) Processing helix chain '4D' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4D 93 " --> pdb=" O LEU4D 89 " (cutoff:3.500A) Processing helix chain '4E' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4E 46 " --> pdb=" O THR4E 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4E 47 " --> pdb=" O TRP4E 43 " (cutoff:3.500A) Proline residue: 4E 49 - end of helix Processing helix chain '4E' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG4E 75 " --> pdb=" O SER4E 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL4E 77 " --> pdb=" O ILE4E 73 " (cutoff:3.500A) Processing helix chain '4E' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR4E 93 " --> pdb=" O LEU4E 89 " (cutoff:3.500A) Processing helix chain '4F' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4F 46 " --> pdb=" O THR4F 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP4F 47 " --> pdb=" O TRP4F 43 " (cutoff:3.500A) Proline residue: 4F 49 - end of helix Processing helix chain '4F' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG4F 75 " --> pdb=" O SER4F 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4F 77 " --> pdb=" O ILE4F 73 " (cutoff:3.500A) Processing helix chain '4F' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4F 93 " --> pdb=" O LEU4F 89 " (cutoff:3.500A) Processing helix chain '4G' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4G 46 " --> pdb=" O THR4G 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP4G 47 " --> pdb=" O TRP4G 43 " (cutoff:3.500A) Proline residue: 4G 49 - end of helix Processing helix chain '4G' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG4G 75 " --> pdb=" O SER4G 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4G 77 " --> pdb=" O ILE4G 73 " (cutoff:3.500A) Processing helix chain '4G' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4G 93 " --> pdb=" O LEU4G 89 " (cutoff:3.500A) Processing helix chain '4H' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR4H 46 " --> pdb=" O THR4H 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4H 47 " --> pdb=" O TRP4H 43 " (cutoff:3.500A) Proline residue: 4H 49 - end of helix Processing helix chain '4H' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG4H 75 " --> pdb=" O SER4H 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4H 77 " --> pdb=" O ILE4H 73 " (cutoff:3.500A) Processing helix chain '4H' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4H 93 " --> pdb=" O LEU4H 89 " (cutoff:3.500A) Processing helix chain '4I' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4I 46 " --> pdb=" O THR4I 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP4I 47 " --> pdb=" O TRP4I 43 " (cutoff:3.500A) Proline residue: 4I 49 - end of helix Processing helix chain '4I' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG4I 75 " --> pdb=" O SER4I 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4I 77 " --> pdb=" O ILE4I 73 " (cutoff:3.500A) Processing helix chain '4I' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4I 93 " --> pdb=" O LEU4I 89 " (cutoff:3.500A) Processing helix chain '4J' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4J 46 " --> pdb=" O THR4J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4J 47 " --> pdb=" O TRP4J 43 " (cutoff:3.500A) Proline residue: 4J 49 - end of helix Processing helix chain '4J' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG4J 75 " --> pdb=" O SER4J 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4J 77 " --> pdb=" O ILE4J 73 " (cutoff:3.500A) Processing helix chain '4J' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR4J 93 " --> pdb=" O LEU4J 89 " (cutoff:3.500A) Processing helix chain '4K' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4K 46 " --> pdb=" O THR4K 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4K 47 " --> pdb=" O TRP4K 43 " (cutoff:3.500A) Proline residue: 4K 49 - end of helix Processing helix chain '4K' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG4K 75 " --> pdb=" O SER4K 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4K 77 " --> pdb=" O ILE4K 73 " (cutoff:3.500A) Processing helix chain '4K' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4K 93 " --> pdb=" O LEU4K 89 " (cutoff:3.500A) Processing helix chain '4L' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4L 46 " --> pdb=" O THR4L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4L 47 " --> pdb=" O TRP4L 43 " (cutoff:3.500A) Proline residue: 4L 49 - end of helix Processing helix chain '4L' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG4L 75 " --> pdb=" O SER4L 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4L 77 " --> pdb=" O ILE4L 73 " (cutoff:3.500A) Processing helix chain '4L' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4L 93 " --> pdb=" O LEU4L 89 " (cutoff:3.500A) Processing helix chain '4M' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR4M 46 " --> pdb=" O THR4M 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4M 47 " --> pdb=" O TRP4M 43 " (cutoff:3.500A) Proline residue: 4M 49 - end of helix Processing helix chain '4M' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG4M 75 " --> pdb=" O SER4M 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL4M 77 " --> pdb=" O ILE4M 73 " (cutoff:3.500A) Processing helix chain '4M' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4M 93 " --> pdb=" O LEU4M 89 " (cutoff:3.500A) Processing helix chain '4N' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR4N 46 " --> pdb=" O THR4N 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4N 47 " --> pdb=" O TRP4N 43 " (cutoff:3.500A) Proline residue: 4N 49 - end of helix Processing helix chain '4N' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG4N 75 " --> pdb=" O SER4N 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL4N 77 " --> pdb=" O ILE4N 73 " (cutoff:3.500A) Processing helix chain '4N' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR4N 93 " --> pdb=" O LEU4N 89 " (cutoff:3.500A) Processing helix chain '5A' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5A 46 " --> pdb=" O THR5A 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5A 47 " --> pdb=" O TRP5A 43 " (cutoff:3.500A) Proline residue: 5A 49 - end of helix Processing helix chain '5A' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG5A 75 " --> pdb=" O SER5A 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5A 77 " --> pdb=" O ILE5A 73 " (cutoff:3.500A) Processing helix chain '5A' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR5A 93 " --> pdb=" O LEU5A 89 " (cutoff:3.500A) Processing helix chain '5B' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5B 46 " --> pdb=" O THR5B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5B 47 " --> pdb=" O TRP5B 43 " (cutoff:3.500A) Proline residue: 5B 49 - end of helix Processing helix chain '5B' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG5B 75 " --> pdb=" O SER5B 71 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL5B 77 " --> pdb=" O ILE5B 73 " (cutoff:3.500A) Processing helix chain '5B' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5B 93 " --> pdb=" O LEU5B 89 " (cutoff:3.500A) Processing helix chain '5C' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5C 46 " --> pdb=" O THR5C 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5C 47 " --> pdb=" O TRP5C 43 " (cutoff:3.500A) Proline residue: 5C 49 - end of helix Processing helix chain '5C' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG5C 75 " --> pdb=" O SER5C 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5C 77 " --> pdb=" O ILE5C 73 " (cutoff:3.500A) Processing helix chain '5C' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5C 93 " --> pdb=" O LEU5C 89 " (cutoff:3.500A) Processing helix chain '5D' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5D 46 " --> pdb=" O THR5D 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5D 47 " --> pdb=" O TRP5D 43 " (cutoff:3.500A) Proline residue: 5D 49 - end of helix Processing helix chain '5D' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG5D 75 " --> pdb=" O SER5D 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5D 77 " --> pdb=" O ILE5D 73 " (cutoff:3.500A) Processing helix chain '5D' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5D 93 " --> pdb=" O LEU5D 89 " (cutoff:3.500A) Processing helix chain '5E' and resid 33 through 65 removed outlier: 3.646A pdb=" N THR5E 46 " --> pdb=" O THR5E 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5E 47 " --> pdb=" O TRP5E 43 " (cutoff:3.500A) Proline residue: 5E 49 - end of helix Processing helix chain '5E' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG5E 75 " --> pdb=" O SER5E 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5E 77 " --> pdb=" O ILE5E 73 " (cutoff:3.500A) Processing helix chain '5E' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5E 93 " --> pdb=" O LEU5E 89 " (cutoff:3.500A) Processing helix chain '5F' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR5F 46 " --> pdb=" O THR5F 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5F 47 " --> pdb=" O TRP5F 43 " (cutoff:3.500A) Proline residue: 5F 49 - end of helix Processing helix chain '5F' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG5F 75 " --> pdb=" O SER5F 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL5F 77 " --> pdb=" O ILE5F 73 " (cutoff:3.500A) Processing helix chain '5F' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR5F 93 " --> pdb=" O LEU5F 89 " (cutoff:3.500A) Processing helix chain '5G' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5G 46 " --> pdb=" O THR5G 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5G 47 " --> pdb=" O TRP5G 43 " (cutoff:3.500A) Proline residue: 5G 49 - end of helix Processing helix chain '5G' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG5G 75 " --> pdb=" O SER5G 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5G 77 " --> pdb=" O ILE5G 73 " (cutoff:3.500A) Processing helix chain '5G' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR5G 93 " --> pdb=" O LEU5G 89 " (cutoff:3.500A) Processing helix chain '5H' and resid 33 through 65 removed outlier: 3.644A pdb=" N THR5H 46 " --> pdb=" O THR5H 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5H 47 " --> pdb=" O TRP5H 43 " (cutoff:3.500A) Proline residue: 5H 49 - end of helix Processing helix chain '5H' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG5H 75 " --> pdb=" O SER5H 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5H 77 " --> pdb=" O ILE5H 73 " (cutoff:3.500A) Processing helix chain '5H' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5H 93 " --> pdb=" O LEU5H 89 " (cutoff:3.500A) Processing helix chain '5I' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5I 46 " --> pdb=" O THR5I 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP5I 47 " --> pdb=" O TRP5I 43 " (cutoff:3.500A) Proline residue: 5I 49 - end of helix Processing helix chain '5I' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG5I 75 " --> pdb=" O SER5I 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL5I 77 " --> pdb=" O ILE5I 73 " (cutoff:3.500A) Processing helix chain '5I' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5I 93 " --> pdb=" O LEU5I 89 " (cutoff:3.500A) Processing helix chain '5J' and resid 33 through 65 removed outlier: 3.646A pdb=" N THR5J 46 " --> pdb=" O THR5J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5J 47 " --> pdb=" O TRP5J 43 " (cutoff:3.500A) Proline residue: 5J 49 - end of helix Processing helix chain '5J' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG5J 75 " --> pdb=" O SER5J 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5J 77 " --> pdb=" O ILE5J 73 " (cutoff:3.500A) Processing helix chain '5J' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5J 93 " --> pdb=" O LEU5J 89 " (cutoff:3.500A) Processing helix chain '5K' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5K 46 " --> pdb=" O THR5K 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP5K 47 " --> pdb=" O TRP5K 43 " (cutoff:3.500A) Proline residue: 5K 49 - end of helix Processing helix chain '5K' and resid 71 through 85 removed outlier: 4.148A pdb=" N ARG5K 75 " --> pdb=" O SER5K 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5K 77 " --> pdb=" O ILE5K 73 " (cutoff:3.500A) Processing helix chain '5K' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5K 93 " --> pdb=" O LEU5K 89 " (cutoff:3.500A) Processing helix chain '5L' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5L 46 " --> pdb=" O THR5L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5L 47 " --> pdb=" O TRP5L 43 " (cutoff:3.500A) Proline residue: 5L 49 - end of helix Processing helix chain '5L' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG5L 75 " --> pdb=" O SER5L 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5L 77 " --> pdb=" O ILE5L 73 " (cutoff:3.500A) Processing helix chain '5L' and resid 85 through 93 removed outlier: 3.590A pdb=" N THR5L 93 " --> pdb=" O LEU5L 89 " (cutoff:3.500A) Processing helix chain '5M' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5M 46 " --> pdb=" O THR5M 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5M 47 " --> pdb=" O TRP5M 43 " (cutoff:3.500A) Proline residue: 5M 49 - end of helix Processing helix chain '5M' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG5M 75 " --> pdb=" O SER5M 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5M 77 " --> pdb=" O ILE5M 73 " (cutoff:3.500A) Processing helix chain '5M' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5M 93 " --> pdb=" O LEU5M 89 " (cutoff:3.500A) Processing helix chain '5N' and resid 33 through 65 removed outlier: 3.645A pdb=" N THR5N 46 " --> pdb=" O THR5N 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5N 47 " --> pdb=" O TRP5N 43 " (cutoff:3.500A) Proline residue: 5N 49 - end of helix Processing helix chain '5N' and resid 71 through 85 removed outlier: 4.147A pdb=" N ARG5N 75 " --> pdb=" O SER5N 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL5N 77 " --> pdb=" O ILE5N 73 " (cutoff:3.500A) Processing helix chain '5N' and resid 85 through 93 removed outlier: 3.589A pdb=" N THR5N 93 " --> pdb=" O LEU5N 89 " (cutoff:3.500A) 2590 hydrogen bonds defined for protein. 7770 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: 7.16 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5461 1.32 - 1.44: 10359 1.44 - 1.56: 23520 1.56 - 1.68: 140 1.68 - 1.80: 560 Bond restraints: 40040 Sorted by residual: bond pdb=" C03 PGW5I 101 " pdb=" O11 PGW5I 101 " ideal model delta sigma weight residual 1.412 1.453 -0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C03 PGW2D 102 " pdb=" O11 PGW2D 102 " ideal model delta sigma weight residual 1.412 1.452 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C03 PGW3J 101 " pdb=" O11 PGW3J 101 " ideal model delta sigma weight residual 1.412 1.452 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C03 PGW4L 101 " pdb=" O11 PGW4L 101 " ideal model delta sigma weight residual 1.412 1.452 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C03 PGW5N 101 " pdb=" O11 PGW5N 101 " ideal model delta sigma weight residual 1.412 1.452 -0.040 2.00e-02 2.50e+03 4.03e+00 ... (remaining 40035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 52121 1.70 - 3.40: 1289 3.40 - 5.10: 329 5.10 - 6.80: 161 6.80 - 8.50: 70 Bond angle restraints: 53970 Sorted by residual: angle pdb=" O11 PGW4D 101 " pdb=" P PGW4D 101 " pdb=" O13 PGW4D 101 " ideal model delta sigma weight residual 111.26 102.76 8.50 3.00e+00 1.11e-01 8.03e+00 angle pdb=" O11 PGW4F 101 " pdb=" P PGW4F 101 " pdb=" O13 PGW4F 101 " ideal model delta sigma weight residual 111.26 102.76 8.50 3.00e+00 1.11e-01 8.02e+00 angle pdb=" O11 PGW1M 101 " pdb=" P PGW1M 101 " pdb=" O13 PGW1M 101 " ideal model delta sigma weight residual 111.26 102.76 8.50 3.00e+00 1.11e-01 8.02e+00 angle pdb=" O11 PGW4N 101 " pdb=" P PGW4N 101 " pdb=" O13 PGW4N 101 " ideal model delta sigma weight residual 111.26 102.77 8.49 3.00e+00 1.11e-01 8.01e+00 angle pdb=" O11 PGW2D 102 " pdb=" P PGW2D 102 " pdb=" O13 PGW2D 102 " ideal model delta sigma weight residual 111.26 102.77 8.49 3.00e+00 1.11e-01 8.01e+00 ... (remaining 53965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 22400 35.76 - 71.51: 910 71.51 - 107.27: 420 107.27 - 143.03: 280 143.03 - 178.79: 70 Dihedral angle restraints: 24080 sinusoidal: 10360 harmonic: 13720 Sorted by residual: dihedral pdb=" C07 PGW1B 102 " pdb=" C06 PGW1B 102 " pdb=" C10 PGW1B 102 " pdb=" C9 PGW1B 102 " ideal model delta sinusoidal sigma weight residual 110.06 -68.73 178.79 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 PGW2E 101 " pdb=" C06 PGW2E 101 " pdb=" C10 PGW2E 101 " pdb=" C9 PGW2E 101 " ideal model delta sinusoidal sigma weight residual 110.06 -68.72 178.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 PGW5N 101 " pdb=" C06 PGW5N 101 " pdb=" C10 PGW5N 101 " pdb=" C9 PGW5N 101 " ideal model delta sinusoidal sigma weight residual 110.06 -68.72 178.78 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 24077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 3064 0.022 - 0.044: 2301 0.044 - 0.066: 652 0.066 - 0.088: 213 0.088 - 0.111: 280 Chirality restraints: 6510 Sorted by residual: chirality pdb=" CA PRO5L 74 " pdb=" N PRO5L 74 " pdb=" C PRO5L 74 " pdb=" CB PRO5L 74 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.06e-01 chirality pdb=" CA PRO4L 74 " pdb=" N PRO4L 74 " pdb=" C PRO4L 74 " pdb=" CB PRO4L 74 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 chirality pdb=" CA PRO3D 49 " pdb=" N PRO3D 49 " pdb=" C PRO3D 49 " pdb=" CB PRO3D 49 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 6507 not shown) Planarity restraints: 6020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW1N 101 " 0.103 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C10 PGW1N 101 " -0.321 2.00e-02 2.50e+03 pdb=" C8 PGW1N 101 " -0.102 2.00e-02 2.50e+03 pdb=" C9 PGW1N 101 " 0.320 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW5L 101 " 0.103 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C10 PGW5L 101 " -0.322 2.00e-02 2.50e+03 pdb=" C8 PGW5L 101 " -0.102 2.00e-02 2.50e+03 pdb=" C9 PGW5L 101 " 0.320 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW5B 101 " 0.103 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C10 PGW5B 101 " -0.321 2.00e-02 2.50e+03 pdb=" C8 PGW5B 101 " -0.102 2.00e-02 2.50e+03 pdb=" C9 PGW5B 101 " 0.320 2.00e-02 2.50e+03 ... (remaining 6017 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 290 2.67 - 3.23: 38159 3.23 - 3.78: 57857 3.78 - 4.34: 86569 4.34 - 4.90: 139738 Nonbonded interactions: 322613 Sorted by model distance: nonbonded pdb=" O TRP3A 43 " pdb=" OG1 THR3A 46 " model vdw 2.109 3.040 nonbonded pdb=" O TRP4K 43 " pdb=" OG1 THR4K 46 " model vdw 2.109 3.040 nonbonded pdb=" O TRP2G 43 " pdb=" OG1 THR2G 46 " model vdw 2.109 3.040 nonbonded pdb=" O TRP3G 43 " pdb=" OG1 THR3G 46 " model vdw 2.109 3.040 nonbonded pdb=" O TRP1E 43 " pdb=" OG1 THR1E 46 " model vdw 2.109 3.040 ... (remaining 322608 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: 0.12 Found NCS groups: ncs_group { reference = chain '1A' selection = chain '2A' selection = chain '3A' selection = chain '4A' selection = chain '5A' } ncs_group { reference = chain '1B' selection = chain '2D' selection = chain '3D' selection = chain '4C' selection = chain '5C' } ncs_group { reference = chain '1C' selection = chain '1D' selection = chain '1E' selection = chain '1F' selection = chain '1G' selection = chain '1H' selection = chain '1I' selection = chain '1J' selection = chain '1K' selection = chain '1L' selection = chain '1M' selection = chain '1N' selection = chain '2B' selection = chain '2C' selection = chain '2E' selection = chain '2F' selection = chain '2G' selection = chain '2H' selection = chain '2I' selection = chain '2J' selection = chain '2K' selection = chain '2L' selection = chain '2M' selection = chain '2N' selection = chain '3B' selection = chain '3C' selection = chain '3E' selection = chain '3F' selection = chain '3G' selection = chain '3H' selection = chain '3I' selection = chain '3J' selection = chain '3K' selection = chain '3L' selection = chain '3M' selection = chain '3N' selection = chain '4B' selection = chain '4D' selection = chain '4E' selection = chain '4F' selection = chain '4G' selection = chain '4H' selection = chain '4I' selection = chain '4J' selection = chain '4K' selection = chain '4L' selection = chain '4M' selection = chain '4N' selection = chain '5B' selection = chain '5D' selection = chain '5E' selection = chain '5F' selection = chain '5G' selection = chain '5H' selection = chain '5I' selection = chain '5J' selection = chain '5K' selection = chain '5L' selection = chain '5M' selection = chain '5N' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.520 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.007 0.041 40040 Z= 0.318 Angle : 0.795 8.504 53970 Z= 0.335 Chirality : 0.038 0.111 6510 Planarity : 0.026 0.238 6020 Dihedral : 28.783 178.787 15260 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.21 (0.12), residues: 4760 helix: 2.48 (0.08), residues: 3710 sheet: None (None), residues: 0 loop : -2.50 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.002 ARG5J 75 TYR 0.003 0.001 TYR5E 88 PHE 0.003 0.001 PHE1H 72 TRP 0.014 0.002 TRP1G 47 HIS 0.001 0.000 HIS1K 66 Details of bonding type rmsd covalent geometry : bond 0.00655 (40040) covalent geometry : angle 0.79549 (53970) hydrogen bonds : bond 0.24579 ( 2590) hydrogen bonds : angle 5.21720 ( 7770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: 1A 56 ILE cc_start: 0.8454 (mt) cc_final: 0.8215 (pt) REVERT: 1F 57 MET cc_start: 0.9017 (ttp) cc_final: 0.8809 (ttp) REVERT: 1L 57 MET cc_start: 0.9022 (ttp) cc_final: 0.8764 (ttm) REVERT: 2B 88 TYR cc_start: 0.9072 (t80) cc_final: 0.8849 (t80) REVERT: 2G 64 MET cc_start: 0.8838 (ttm) cc_final: 0.8574 (ttp) REVERT: 2H 64 MET cc_start: 0.8877 (ttm) cc_final: 0.8604 (ttp) REVERT: 2L 64 MET cc_start: 0.8775 (ttm) cc_final: 0.8555 (ttp) REVERT: 2N 57 MET cc_start: 0.8605 (ttp) cc_final: 0.8259 (ttm) REVERT: 3H 30 THR cc_start: 0.8975 (p) cc_final: 0.8727 (p) REVERT: 3J 64 MET cc_start: 0.8866 (ttm) cc_final: 0.8650 (ttp) REVERT: 3L 57 MET cc_start: 0.8955 (ttp) cc_final: 0.8741 (ttm) REVERT: 3N 88 TYR cc_start: 0.9141 (t80) cc_final: 0.8851 (t80) REVERT: 4L 57 MET cc_start: 0.8930 (ttp) cc_final: 0.8715 (ttm) REVERT: 5A 56 ILE cc_start: 0.8378 (mt) cc_final: 0.8088 (pt) REVERT: 5C 30 THR cc_start: 0.8874 (p) cc_final: 0.8591 (p) REVERT: 5F 57 MET cc_start: 0.8886 (ttp) cc_final: 0.8559 (ttm) REVERT: 5I 57 MET cc_start: 0.8925 (ttp) cc_final: 0.8655 (ttm) REVERT: 5L 62 MET cc_start: 0.8747 (mmp) cc_final: 0.8524 (mmp) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.7633 time to fit residues: 465.6683 Evaluate side-chains 397 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 0.1980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.075045 restraints weight = 45496.213| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 1.61 r_work: 0.2627 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 40040 Z= 0.131 Angle : 0.509 5.103 53970 Z= 0.257 Chirality : 0.041 0.130 6510 Planarity : 0.005 0.034 6020 Dihedral : 26.305 89.849 8260 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.70 % Allowed : 5.19 % Favored : 94.11 % 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: 3.32 (0.12), residues: 4760 helix: 2.86 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.31 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG2H 75 TYR 0.010 0.001 TYR4N 88 PHE 0.004 0.001 PHE4J 72 TRP 0.012 0.001 TRP5A 43 HIS 0.012 0.002 HIS1G 66 Details of bonding type rmsd covalent geometry : bond 0.00267 (40040) covalent geometry : angle 0.50865 (53970) hydrogen bonds : bond 0.05387 ( 2590) hydrogen bonds : angle 3.62208 ( 7770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 577 time to evaluate : 1.476 Fit side-chains REVERT: 1B 75 ARG cc_start: 0.6699 (ttp-170) cc_final: 0.6443 (ttm110) REVERT: 2E 66 HIS cc_start: 0.8486 (m-70) cc_final: 0.8193 (m170) REVERT: 2G 64 MET cc_start: 0.8854 (ttm) cc_final: 0.8547 (ttp) REVERT: 3B 75 ARG cc_start: 0.6808 (ttm170) cc_final: 0.6570 (ttm170) REVERT: 3E 62 MET cc_start: 0.8732 (mmm) cc_final: 0.8521 (mmp) REVERT: 3H 30 THR cc_start: 0.8950 (p) cc_final: 0.8731 (p) REVERT: 3K 88 TYR cc_start: 0.8858 (t80) cc_final: 0.8653 (t80) REVERT: 4A 62 MET cc_start: 0.6575 (OUTLIER) cc_final: 0.6368 (mmm) REVERT: 5C 30 THR cc_start: 0.8749 (p) cc_final: 0.8445 (p) REVERT: 5H 62 MET cc_start: 0.8838 (mmp) cc_final: 0.8555 (mmp) REVERT: 5L 62 MET cc_start: 0.8809 (mmp) cc_final: 0.8544 (mmp) outliers start: 28 outliers final: 4 residues processed: 586 average time/residue: 0.5721 time to fit residues: 428.3321 Evaluate side-chains 477 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 472 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2B residue 59 SER Chi-restraints excluded: chain 4A residue 62 MET Chi-restraints excluded: chain 4B residue 59 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5B residue 59 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 464 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 455 optimal weight: 6.9990 chunk 418 optimal weight: 4.9990 chunk 411 optimal weight: 9.9990 chunk 74 optimal weight: 0.0070 chunk 461 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 234 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1C 66 HIS 1F 66 HIS ** 3B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4C 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.100745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.072840 restraints weight = 45539.151| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 1.59 r_work: 0.2596 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 40040 Z= 0.146 Angle : 0.489 5.795 53970 Z= 0.244 Chirality : 0.041 0.132 6510 Planarity : 0.004 0.033 6020 Dihedral : 23.797 89.975 8260 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.38 % Allowed : 7.49 % Favored : 91.13 % 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: 3.77 (0.13), residues: 4760 helix: 3.23 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.43 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG5A 75 TYR 0.007 0.001 TYR1M 88 PHE 0.007 0.001 PHE4K 61 TRP 0.010 0.001 TRP4D 47 HIS 0.023 0.001 HIS2E 66 Details of bonding type rmsd covalent geometry : bond 0.00336 (40040) covalent geometry : angle 0.48872 (53970) hydrogen bonds : bond 0.05717 ( 2590) hydrogen bonds : angle 3.31896 ( 7770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 523 time to evaluate : 1.274 Fit side-chains REVERT: 1A 45 SER cc_start: 0.8722 (m) cc_final: 0.8396 (p) REVERT: 3A 45 SER cc_start: 0.8703 (m) cc_final: 0.8474 (m) REVERT: 3H 30 THR cc_start: 0.8969 (p) cc_final: 0.8754 (p) REVERT: 3H 64 MET cc_start: 0.8950 (ttm) cc_final: 0.8736 (ttp) REVERT: 3N 88 TYR cc_start: 0.8508 (t80) cc_final: 0.8105 (t80) REVERT: 4A 62 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6513 (mmm) REVERT: 4C 71 SER cc_start: 0.8609 (p) cc_final: 0.8201 (m) REVERT: 4M 88 TYR cc_start: 0.8686 (t80) cc_final: 0.8431 (t80) REVERT: 5A 42 THR cc_start: 0.8527 (m) cc_final: 0.8163 (p) REVERT: 5C 71 SER cc_start: 0.8760 (p) cc_final: 0.8395 (m) REVERT: 5H 62 MET cc_start: 0.8899 (mmp) cc_final: 0.8611 (mmp) REVERT: 5J 62 MET cc_start: 0.9162 (mmp) cc_final: 0.8949 (mmp) REVERT: 5L 62 MET cc_start: 0.8840 (mmp) cc_final: 0.8595 (mmp) outliers start: 55 outliers final: 36 residues processed: 560 average time/residue: 0.5576 time to fit residues: 399.8330 Evaluate side-chains 519 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 482 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 91 SER Chi-restraints excluded: chain 1D residue 91 SER Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 1H residue 91 SER Chi-restraints excluded: chain 1L residue 91 SER Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2D residue 91 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 2M residue 76 ILE Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3G residue 91 SER Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 3I residue 91 SER Chi-restraints excluded: chain 3J residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4A residue 62 MET Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4F residue 91 SER Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 4I residue 91 SER Chi-restraints excluded: chain 4J residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5A residue 64 MET Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5D residue 91 SER Chi-restraints excluded: chain 5E residue 91 SER Chi-restraints excluded: chain 5F residue 91 SER Chi-restraints excluded: chain 5H residue 91 SER Chi-restraints excluded: chain 5I residue 91 SER Chi-restraints excluded: chain 5J residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 333 optimal weight: 0.6980 chunk 230 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 402 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 484 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1C 66 HIS 1E 66 HIS 1G 66 HIS 2G 66 HIS 2H 66 HIS 3H 66 HIS 3J 66 HIS 3L 66 HIS 4C 66 HIS 4D 66 HIS 4E 66 HIS 4G 66 HIS ** 5B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5E 66 HIS 5G 66 HIS 5J 66 HIS 5L 66 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.075846 restraints weight = 44352.368| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 1.49 r_work: 0.2596 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 40040 Z= 0.164 Angle : 0.546 6.044 53970 Z= 0.261 Chirality : 0.043 0.141 6510 Planarity : 0.004 0.039 6020 Dihedral : 20.986 82.733 8260 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.40 % Allowed : 8.47 % Favored : 90.13 % 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: 3.70 (0.13), residues: 4760 helix: 3.20 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.60 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG1H 75 TYR 0.007 0.001 TYR5D 88 PHE 0.006 0.001 PHE4K 61 TRP 0.012 0.001 TRP4D 47 HIS 0.015 0.001 HIS3B 66 Details of bonding type rmsd covalent geometry : bond 0.00396 (40040) covalent geometry : angle 0.54592 (53970) hydrogen bonds : bond 0.05594 ( 2590) hydrogen bonds : angle 3.35065 ( 7770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 525 time to evaluate : 1.394 Fit side-chains revert: symmetry clash REVERT: 1A 45 SER cc_start: 0.8748 (m) cc_final: 0.8456 (p) REVERT: 2A 75 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5592 (ttp80) REVERT: 2C 71 SER cc_start: 0.8781 (p) cc_final: 0.8432 (m) REVERT: 2K 31 ASP cc_start: 0.8694 (t0) cc_final: 0.8474 (t0) REVERT: 2M 71 SER cc_start: 0.9093 (p) cc_final: 0.8857 (m) REVERT: 3A 45 SER cc_start: 0.8708 (m) cc_final: 0.8480 (m) REVERT: 3N 88 TYR cc_start: 0.8608 (t80) cc_final: 0.8203 (t80) REVERT: 4B 75 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6932 (ttm-80) REVERT: 4C 71 SER cc_start: 0.8715 (p) cc_final: 0.8354 (m) REVERT: 4C 90 VAL cc_start: 0.8504 (t) cc_final: 0.8209 (t) REVERT: 5A 75 ARG cc_start: 0.5983 (OUTLIER) cc_final: 0.5604 (ttp80) REVERT: 5C 71 SER cc_start: 0.8769 (p) cc_final: 0.8430 (m) outliers start: 56 outliers final: 32 residues processed: 564 average time/residue: 0.5681 time to fit residues: 411.0912 Evaluate side-chains 520 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 485 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 75 ARG Chi-restraints excluded: chain 1C residue 91 SER Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2B residue 59 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3D residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3G residue 91 SER Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4A residue 62 MET Chi-restraints excluded: chain 4B residue 75 ARG Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4F residue 91 SER Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 4I residue 91 SER Chi-restraints excluded: chain 4J residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5A residue 64 MET Chi-restraints excluded: chain 5A residue 75 ARG Chi-restraints excluded: chain 5A residue 76 ILE Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5B residue 91 SER Chi-restraints excluded: chain 5D residue 91 SER Chi-restraints excluded: chain 5E residue 91 SER Chi-restraints excluded: chain 5F residue 91 SER Chi-restraints excluded: chain 5J residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 157 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 469 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 453 optimal weight: 5.9990 chunk 383 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1G 66 HIS 1N 66 HIS 2H 66 HIS ** 3B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3J 66 HIS 4D 66 HIS 4E 66 HIS 4G 66 HIS 5B 66 HIS 5C 66 HIS 5E 66 HIS 5G 66 HIS 5I 66 HIS 5J 66 HIS 5L 66 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.072350 restraints weight = 45477.267| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 1.58 r_work: 0.2581 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 40040 Z= 0.167 Angle : 0.522 6.617 53970 Z= 0.255 Chirality : 0.043 0.131 6510 Planarity : 0.004 0.031 6020 Dihedral : 19.421 81.914 8260 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.40 % Allowed : 8.77 % Favored : 89.82 % 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: 3.63 (0.12), residues: 4760 helix: 3.16 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.69 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG1H 75 TYR 0.009 0.001 TYR4M 88 PHE 0.006 0.001 PHE2J 61 TRP 0.011 0.001 TRP5D 47 HIS 0.006 0.001 HIS5B 66 Details of bonding type rmsd covalent geometry : bond 0.00403 (40040) covalent geometry : angle 0.52227 (53970) hydrogen bonds : bond 0.05770 ( 2590) hydrogen bonds : angle 3.34435 ( 7770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 522 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: 1A 45 SER cc_start: 0.8694 (m) cc_final: 0.8400 (p) REVERT: 2A 75 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5432 (ttp80) REVERT: 2C 71 SER cc_start: 0.8730 (p) cc_final: 0.8430 (m) REVERT: 2D 75 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7277 (ttm170) REVERT: 2M 71 SER cc_start: 0.9017 (p) cc_final: 0.8797 (m) REVERT: 3A 45 SER cc_start: 0.8647 (m) cc_final: 0.8418 (m) REVERT: 3A 75 ARG cc_start: 0.6393 (OUTLIER) cc_final: 0.5795 (ttp80) REVERT: 3M 90 VAL cc_start: 0.8517 (t) cc_final: 0.8224 (t) REVERT: 3N 88 TYR cc_start: 0.8550 (t80) cc_final: 0.8118 (t80) REVERT: 4C 71 SER cc_start: 0.8642 (p) cc_final: 0.8324 (m) REVERT: 4C 90 VAL cc_start: 0.8420 (t) cc_final: 0.8154 (t) REVERT: 4F 75 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8224 (ttm170) REVERT: 5C 71 SER cc_start: 0.8771 (p) cc_final: 0.8473 (m) outliers start: 56 outliers final: 34 residues processed: 564 average time/residue: 0.5960 time to fit residues: 426.4935 Evaluate side-chains 524 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 486 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 75 ARG Chi-restraints excluded: chain 1C residue 91 SER Chi-restraints excluded: chain 1D residue 91 SER Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 1L residue 64 MET Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2C residue 91 SER Chi-restraints excluded: chain 2D residue 75 ARG Chi-restraints excluded: chain 2D residue 91 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3A residue 75 ARG Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3D residue 30 THR Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3G residue 91 SER Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 3I residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4A residue 62 MET Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4F residue 75 ARG Chi-restraints excluded: chain 4F residue 91 SER Chi-restraints excluded: chain 4I residue 91 SER Chi-restraints excluded: chain 4J residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5B residue 91 SER Chi-restraints excluded: chain 5E residue 91 SER Chi-restraints excluded: chain 5F residue 91 SER Chi-restraints excluded: chain 5I residue 91 SER Chi-restraints excluded: chain 5J residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 469 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 435 optimal weight: 3.9990 chunk 224 optimal weight: 0.0570 chunk 432 optimal weight: 0.9990 chunk 265 optimal weight: 0.7980 chunk 243 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 475 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1F 66 HIS 2A 41 GLN 2H 66 HIS 3A 41 GLN 3B 66 HIS 4C 66 HIS 5B 66 HIS 5G 66 HIS 5I 66 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.103506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.075982 restraints weight = 45401.008| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.59 r_work: 0.2651 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 40040 Z= 0.104 Angle : 0.425 5.630 53970 Z= 0.208 Chirality : 0.040 0.120 6510 Planarity : 0.004 0.031 6020 Dihedral : 18.191 81.740 8260 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.75 % Allowed : 9.80 % Favored : 89.45 % 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: 4.09 (0.12), residues: 4760 helix: 3.48 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.54 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG2J 75 TYR 0.007 0.001 TYR1M 88 PHE 0.005 0.001 PHE1A 72 TRP 0.011 0.001 TRP2J 47 HIS 0.004 0.001 HIS1B 66 Details of bonding type rmsd covalent geometry : bond 0.00209 (40040) covalent geometry : angle 0.42477 (53970) hydrogen bonds : bond 0.04004 ( 2590) hydrogen bonds : angle 3.10839 ( 7770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 555 time to evaluate : 1.314 Fit side-chains REVERT: 1A 45 SER cc_start: 0.8674 (m) cc_final: 0.8392 (p) REVERT: 1L 45 SER cc_start: 0.9000 (m) cc_final: 0.8758 (p) REVERT: 2A 75 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5545 (ttp80) REVERT: 2B 75 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6453 (ttm110) REVERT: 2C 71 SER cc_start: 0.8609 (p) cc_final: 0.8330 (m) REVERT: 3L 64 MET cc_start: 0.8888 (ttp) cc_final: 0.8672 (ttm) REVERT: 3N 88 TYR cc_start: 0.8514 (t80) cc_final: 0.8049 (t80) REVERT: 4A 75 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5072 (ttm170) REVERT: 4C 71 SER cc_start: 0.8520 (p) cc_final: 0.8269 (m) REVERT: 4F 75 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8200 (ttm170) REVERT: 5A 42 THR cc_start: 0.8493 (m) cc_final: 0.8140 (p) outliers start: 30 outliers final: 16 residues processed: 575 average time/residue: 0.5447 time to fit residues: 402.4555 Evaluate side-chains 539 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 519 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 91 SER Chi-restraints excluded: chain 1H residue 64 MET Chi-restraints excluded: chain 1M residue 76 ILE Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2B residue 75 ARG Chi-restraints excluded: chain 2D residue 91 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 3D residue 64 MET Chi-restraints excluded: chain 4A residue 62 MET Chi-restraints excluded: chain 4A residue 75 ARG Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4F residue 75 ARG Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5B residue 91 SER Chi-restraints excluded: chain 5D residue 91 SER Chi-restraints excluded: chain 5G residue 91 SER Chi-restraints excluded: chain 5H residue 91 SER Chi-restraints excluded: chain 5I residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 369 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 361 optimal weight: 0.5980 chunk 388 optimal weight: 8.9990 chunk 324 optimal weight: 2.9990 chunk 489 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 360 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 194 optimal weight: 10.0000 chunk 277 optimal weight: 0.2980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1D 66 HIS 1F 66 HIS 2A 41 GLN 2E 66 HIS 2H 66 HIS 3A 41 GLN 3H 66 HIS 4C 66 HIS 4E 66 HIS 4I 66 HIS 5B 66 HIS 5G 66 HIS 5I 66 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.102076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.074890 restraints weight = 45408.902| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 1.53 r_work: 0.2637 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 40040 Z= 0.117 Angle : 0.449 6.841 53970 Z= 0.220 Chirality : 0.041 0.120 6510 Planarity : 0.004 0.029 6020 Dihedral : 17.976 79.604 8260 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.75 % Allowed : 10.15 % Favored : 89.10 % 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: 4.06 (0.12), residues: 4760 helix: 3.47 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.58 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG3J 75 TYR 0.008 0.001 TYR5D 88 PHE 0.003 0.001 PHE4H 61 TRP 0.009 0.001 TRP4C 47 HIS 0.006 0.001 HIS5B 66 Details of bonding type rmsd covalent geometry : bond 0.00258 (40040) covalent geometry : angle 0.44948 (53970) hydrogen bonds : bond 0.04536 ( 2590) hydrogen bonds : angle 3.08329 ( 7770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 514 time to evaluate : 1.334 Fit side-chains REVERT: 1A 45 SER cc_start: 0.8722 (m) cc_final: 0.8431 (p) REVERT: 2A 75 ARG cc_start: 0.6115 (OUTLIER) cc_final: 0.5524 (ttp80) REVERT: 2C 71 SER cc_start: 0.8659 (p) cc_final: 0.8382 (m) REVERT: 3L 64 MET cc_start: 0.8986 (ttp) cc_final: 0.8749 (ttm) REVERT: 3M 90 VAL cc_start: 0.8566 (t) cc_final: 0.8301 (t) REVERT: 3N 88 TYR cc_start: 0.8538 (t80) cc_final: 0.8097 (t80) REVERT: 4A 75 ARG cc_start: 0.6219 (OUTLIER) cc_final: 0.5146 (ttm170) REVERT: 4C 71 SER cc_start: 0.8575 (p) cc_final: 0.8316 (m) REVERT: 4F 75 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8271 (ttm170) REVERT: 5A 42 THR cc_start: 0.8512 (m) cc_final: 0.8115 (p) outliers start: 30 outliers final: 14 residues processed: 534 average time/residue: 0.5465 time to fit residues: 373.4022 Evaluate side-chains 516 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 499 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1H residue 64 MET Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2C residue 30 THR Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 4A residue 62 MET Chi-restraints excluded: chain 4A residue 75 ARG Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4F residue 75 ARG Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5B residue 91 SER Chi-restraints excluded: chain 5H residue 91 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 470 optimal weight: 4.9990 chunk 263 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 375 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 357 optimal weight: 0.0000 chunk 473 optimal weight: 0.0770 chunk 448 optimal weight: 10.0000 chunk 480 optimal weight: 0.8980 chunk 178 optimal weight: 0.0970 chunk 471 optimal weight: 0.9980 overall best weight: 0.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2A 41 GLN 2H 66 HIS 3A 41 GLN 4I 66 HIS 5B 66 HIS 5I 66 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.106918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.079674 restraints weight = 44945.020| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.57 r_work: 0.2712 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 40040 Z= 0.095 Angle : 0.409 5.911 53970 Z= 0.197 Chirality : 0.040 0.119 6510 Planarity : 0.004 0.029 6020 Dihedral : 17.332 80.211 8260 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.48 % Allowed : 10.25 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.30 (0.12), residues: 4760 helix: 3.62 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.42 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG1D 75 TYR 0.007 0.001 TYR1B 88 PHE 0.004 0.001 PHE2A 61 TRP 0.011 0.001 TRP2J 47 HIS 0.003 0.001 HIS5B 66 Details of bonding type rmsd covalent geometry : bond 0.00180 (40040) covalent geometry : angle 0.40903 (53970) hydrogen bonds : bond 0.03382 ( 2590) hydrogen bonds : angle 2.85618 ( 7770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 548 time to evaluate : 1.205 Fit side-chains REVERT: 1A 45 SER cc_start: 0.8632 (m) cc_final: 0.8425 (p) REVERT: 1I 64 MET cc_start: 0.8996 (ttm) cc_final: 0.8709 (ttp) REVERT: 1M 71 SER cc_start: 0.8757 (p) cc_final: 0.8536 (m) REVERT: 2A 75 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5598 (ttp80) REVERT: 2C 71 SER cc_start: 0.8658 (p) cc_final: 0.8331 (m) REVERT: 3B 41 GLN cc_start: 0.8827 (tt0) cc_final: 0.8600 (tt0) REVERT: 3K 45 SER cc_start: 0.8870 (m) cc_final: 0.8661 (p) REVERT: 3M 71 SER cc_start: 0.8751 (p) cc_final: 0.8435 (m) REVERT: 3N 88 TYR cc_start: 0.8462 (t80) cc_final: 0.8021 (t80) REVERT: 4A 42 THR cc_start: 0.8480 (m) cc_final: 0.7998 (p) REVERT: 4A 75 ARG cc_start: 0.6100 (OUTLIER) cc_final: 0.5016 (ttm170) REVERT: 4F 75 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8029 (ttm170) REVERT: 4I 64 MET cc_start: 0.9011 (ttm) cc_final: 0.8705 (ttm) REVERT: 5A 42 THR cc_start: 0.8496 (m) cc_final: 0.8149 (p) REVERT: 5K 71 SER cc_start: 0.8793 (p) cc_final: 0.8514 (m) REVERT: 5N 59 SER cc_start: 0.8891 (m) cc_final: 0.8605 (m) outliers start: 19 outliers final: 8 residues processed: 560 average time/residue: 0.4967 time to fit residues: 357.2382 Evaluate side-chains 534 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 523 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2C residue 30 THR Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4A residue 75 ARG Chi-restraints excluded: chain 4F residue 75 ARG Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 5A residue 76 ILE Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5H residue 91 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 254 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 447 optimal weight: 1.9990 chunk 27 optimal weight: 0.0270 chunk 284 optimal weight: 0.8980 chunk 415 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2A 41 GLN 2E 66 HIS 2H 66 HIS 3A 41 GLN 4D 66 HIS 4I 66 HIS 5E 66 HIS 5I 66 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.076066 restraints weight = 45158.804| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 1.58 r_work: 0.2654 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 40040 Z= 0.117 Angle : 0.453 7.193 53970 Z= 0.220 Chirality : 0.041 0.119 6510 Planarity : 0.004 0.027 6020 Dihedral : 17.413 79.976 8260 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.53 % Allowed : 10.48 % Favored : 89.00 % 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: 4.16 (0.12), residues: 4760 helix: 3.53 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.51 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG3F 75 TYR 0.006 0.001 TYR5M 88 PHE 0.003 0.001 PHE4H 61 TRP 0.008 0.001 TRP4C 47 HIS 0.003 0.001 HIS3B 66 Details of bonding type rmsd covalent geometry : bond 0.00263 (40040) covalent geometry : angle 0.45325 (53970) hydrogen bonds : bond 0.04372 ( 2590) hydrogen bonds : angle 2.96176 ( 7770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 515 time to evaluate : 1.363 Fit side-chains REVERT: 1A 45 SER cc_start: 0.8686 (m) cc_final: 0.8417 (p) REVERT: 2A 42 THR cc_start: 0.8440 (m) cc_final: 0.8219 (p) REVERT: 2A 75 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5574 (ttp80) REVERT: 2B 75 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6239 (ttm110) REVERT: 2C 71 SER cc_start: 0.8718 (p) cc_final: 0.8373 (m) REVERT: 3M 90 VAL cc_start: 0.8538 (t) cc_final: 0.8275 (t) REVERT: 3N 88 TYR cc_start: 0.8453 (t80) cc_final: 0.8034 (t80) REVERT: 4B 75 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6574 (ttm110) REVERT: 4F 75 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8094 (ttm170) REVERT: 4K 64 MET cc_start: 0.9119 (ttm) cc_final: 0.8807 (ttp) REVERT: 5A 42 THR cc_start: 0.8495 (m) cc_final: 0.8102 (p) REVERT: 5K 71 SER cc_start: 0.8896 (p) cc_final: 0.8599 (m) REVERT: 5N 59 SER cc_start: 0.8854 (m) cc_final: 0.8570 (m) outliers start: 21 outliers final: 13 residues processed: 530 average time/residue: 0.5032 time to fit residues: 341.3413 Evaluate side-chains 519 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 502 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1C residue 91 SER Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2B residue 75 ARG Chi-restraints excluded: chain 2C residue 30 THR Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4B residue 75 ARG Chi-restraints excluded: chain 4F residue 75 ARG Chi-restraints excluded: chain 4J residue 91 SER Chi-restraints excluded: chain 5A residue 76 ILE Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5G residue 91 SER Chi-restraints excluded: chain 5H residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 167 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 382 optimal weight: 1.9990 chunk 428 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 62 optimal weight: 0.0970 chunk 417 optimal weight: 0.0970 chunk 270 optimal weight: 0.5980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1B 66 HIS 2A 41 GLN 2H 66 HIS 3A 41 GLN 4C 66 HIS 4I 66 HIS 5I 66 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.104849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.077601 restraints weight = 44940.829| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.57 r_work: 0.2679 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 40040 Z= 0.102 Angle : 0.432 7.768 53970 Z= 0.208 Chirality : 0.040 0.118 6510 Planarity : 0.004 0.027 6020 Dihedral : 17.273 80.817 8260 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.50 % Allowed : 10.55 % Favored : 88.95 % 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: 4.22 (0.12), residues: 4760 helix: 3.57 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.48 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG3F 75 TYR 0.006 0.001 TYR5N 88 PHE 0.003 0.001 PHE4M 72 TRP 0.009 0.001 TRP4H 47 HIS 0.007 0.001 HIS1B 66 Details of bonding type rmsd covalent geometry : bond 0.00210 (40040) covalent geometry : angle 0.43154 (53970) hydrogen bonds : bond 0.03917 ( 2590) hydrogen bonds : angle 2.93218 ( 7770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 517 time to evaluate : 1.181 Fit side-chains REVERT: 1A 45 SER cc_start: 0.8681 (m) cc_final: 0.8418 (p) REVERT: 2A 42 THR cc_start: 0.8451 (m) cc_final: 0.8205 (p) REVERT: 2A 75 ARG cc_start: 0.6135 (OUTLIER) cc_final: 0.5602 (ttp80) REVERT: 2B 75 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6271 (ttm110) REVERT: 2C 71 SER cc_start: 0.8692 (p) cc_final: 0.8359 (m) REVERT: 3M 71 SER cc_start: 0.8849 (p) cc_final: 0.8551 (m) REVERT: 3N 88 TYR cc_start: 0.8454 (t80) cc_final: 0.8041 (t80) REVERT: 4A 42 THR cc_start: 0.8483 (m) cc_final: 0.7991 (p) REVERT: 4A 75 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.5024 (ttm170) REVERT: 4C 90 VAL cc_start: 0.8344 (t) cc_final: 0.8120 (t) REVERT: 4F 75 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8112 (ttm170) REVERT: 4K 64 MET cc_start: 0.9107 (ttm) cc_final: 0.8847 (ttp) REVERT: 5A 42 THR cc_start: 0.8523 (m) cc_final: 0.8149 (p) REVERT: 5K 71 SER cc_start: 0.8835 (p) cc_final: 0.8580 (m) REVERT: 5N 59 SER cc_start: 0.8900 (m) cc_final: 0.8655 (m) outliers start: 20 outliers final: 14 residues processed: 531 average time/residue: 0.4977 time to fit residues: 338.5907 Evaluate side-chains 529 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 511 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 80 LEU Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2B residue 75 ARG Chi-restraints excluded: chain 2C residue 30 THR Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4A residue 75 ARG Chi-restraints excluded: chain 4F residue 75 ARG Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 4J residue 91 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5A residue 76 ILE Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5H residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 101 optimal weight: 10.0000 chunk 384 optimal weight: 7.9990 chunk 446 optimal weight: 5.9990 chunk 367 optimal weight: 8.9990 chunk 459 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 chunk 458 optimal weight: 5.9990 chunk 401 optimal weight: 0.5980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1B 66 HIS 1D 66 HIS 2A 41 GLN 2E 66 HIS 2H 66 HIS 3A 41 GLN 3J 66 HIS 4C 66 HIS 4D 66 HIS 5D 66 HIS 5E 66 HIS 5G 66 HIS 5I 66 HIS 5L 66 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.099924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.072839 restraints weight = 45766.839| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 1.53 r_work: 0.2594 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 40040 Z= 0.158 Angle : 0.519 8.534 53970 Z= 0.253 Chirality : 0.042 0.134 6510 Planarity : 0.004 0.027 6020 Dihedral : 17.940 80.897 8260 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.75 % Allowed : 10.38 % Favored : 88.87 % 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: 3.87 (0.12), residues: 4760 helix: 3.32 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.57 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG3F 75 TYR 0.008 0.001 TYR5N 88 PHE 0.006 0.001 PHE2J 61 TRP 0.015 0.001 TRP3C 63 HIS 0.011 0.001 HIS1B 66 Details of bonding type rmsd covalent geometry : bond 0.00377 (40040) covalent geometry : angle 0.51868 (53970) hydrogen bonds : bond 0.05610 ( 2590) hydrogen bonds : angle 3.23281 ( 7770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10637.85 seconds wall clock time: 182 minutes 45.84 seconds (10965.84 seconds total)