Starting phenix.real_space_refine on Thu Dec 26 10:28:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cw4_27023/12_2024/8cw4_27023_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cw4_27023/12_2024/8cw4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cw4_27023/12_2024/8cw4_27023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cw4_27023/12_2024/8cw4_27023.map" model { file = "/net/cci-nas-00/data/ceres_data/8cw4_27023/12_2024/8cw4_27023_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cw4_27023/12_2024/8cw4_27023_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 21.78, per 1000 atoms: 0.55 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: 11.55 Conformation dependent library (CDL) restraints added in 5.4 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: 3.15 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: 13.13 Time building geometry restraints manager: 12.91 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: 0.00 Found NCS groups: ncs_group { reference = chain '1A' selection = (chain '1B' and resid 28 through 97) selection = (chain '1C' and resid 28 through 97) selection = (chain '1D' and resid 28 through 97) selection = (chain '1E' and resid 28 through 97) selection = (chain '1F' and resid 28 through 97) selection = (chain '1G' and resid 28 through 97) selection = (chain '1H' and resid 28 through 97) selection = (chain '1I' and resid 28 through 97) selection = (chain '1J' and resid 28 through 97) selection = (chain '1K' and resid 28 through 97) selection = (chain '1L' and resid 28 through 97) selection = (chain '1M' and resid 28 through 97) selection = (chain '1N' and resid 28 through 97) selection = chain '2A' selection = (chain '2B' and resid 28 through 97) selection = (chain '2C' and resid 28 through 97) selection = (chain '2D' and resid 28 through 97) selection = (chain '2E' and resid 28 through 97) selection = (chain '2F' and resid 28 through 97) selection = (chain '2G' and resid 28 through 97) selection = (chain '2H' and resid 28 through 97) selection = (chain '2I' and resid 28 through 97) selection = (chain '2J' and resid 28 through 97) selection = (chain '2K' and resid 28 through 97) selection = (chain '2L' and resid 28 through 97) selection = (chain '2M' and resid 28 through 97) selection = (chain '2N' and resid 28 through 97) selection = chain '3A' selection = (chain '3B' and resid 28 through 97) selection = (chain '3C' and resid 28 through 97) selection = (chain '3D' and resid 28 through 97) selection = (chain '3E' and resid 28 through 97) selection = (chain '3F' and resid 28 through 97) selection = (chain '3G' and resid 28 through 97) selection = (chain '3H' and resid 28 through 97) selection = (chain '3I' and resid 28 through 97) selection = (chain '3J' and resid 28 through 97) selection = (chain '3K' and resid 28 through 97) selection = (chain '3L' and resid 28 through 97) selection = (chain '3M' and resid 28 through 97) selection = (chain '3N' and resid 28 through 97) selection = chain '4A' selection = (chain '4B' and resid 28 through 97) selection = (chain '4C' and resid 28 through 97) selection = (chain '4D' and resid 28 through 97) selection = (chain '4E' and resid 28 through 97) selection = (chain '4F' and resid 28 through 97) selection = (chain '4G' and resid 28 through 97) selection = (chain '4H' and resid 28 through 97) selection = (chain '4I' and resid 28 through 97) selection = (chain '4J' and resid 28 through 97) selection = (chain '4K' and resid 28 through 97) selection = (chain '4L' and resid 28 through 97) selection = (chain '4M' and resid 28 through 97) selection = (chain '4N' and resid 28 through 97) selection = chain '5A' selection = (chain '5B' and resid 28 through 97) selection = (chain '5C' and resid 28 through 97) selection = (chain '5D' and resid 28 through 97) selection = (chain '5E' and resid 28 through 97) selection = (chain '5F' and resid 28 through 97) selection = (chain '5G' and resid 28 through 97) selection = (chain '5H' and resid 28 through 97) selection = (chain '5I' and resid 28 through 97) selection = (chain '5J' and resid 28 through 97) selection = (chain '5K' and resid 28 through 97) selection = (chain '5L' and resid 28 through 97) selection = (chain '5M' and resid 28 through 97) selection = (chain '5N' and resid 28 through 97) } 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: 0.940 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: 0.040 Extract box with map and model: 1.630 Check model and map are aligned: 0.320 Set scattering table: 0.370 Process input model: 81.800 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.450 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: 0.020 Load rotamer database and sin/cos tables:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.160 ------------------------------------------------------------------------------- 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= 0.421 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP1G 47 HIS 0.001 0.000 HIS1K 66 PHE 0.003 0.001 PHE1H 72 TYR 0.003 0.001 TYR5E 88 ARG 0.004 0.002 ARG5J 75 *********************** 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 : 4.457 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: 1.6297 time to fit residues: 995.0248 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 : 4.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 413 optimal weight: 0.2980 chunk 371 optimal weight: 0.0570 chunk 206 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 384 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 chunk 285 optimal weight: 0.5980 chunk 444 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1G 66 HIS 4E 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 40040 Z= 0.168 Angle : 0.496 5.034 53970 Z= 0.253 Chirality : 0.041 0.123 6510 Planarity : 0.005 0.032 6020 Dihedral : 26.257 88.080 8260 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.63 % Allowed : 5.39 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.12), residues: 4760 helix: 3.03 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.29 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP5A 43 HIS 0.010 0.002 HIS1B 66 PHE 0.005 0.001 PHE2A 72 TYR 0.009 0.001 TYR4N 88 ARG 0.003 0.001 ARG2H 75 *********************** 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 604 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 579 time to evaluate : 4.328 Fit side-chains REVERT: 1K 64 MET cc_start: 0.8588 (ttm) cc_final: 0.8360 (ttp) REVERT: 1M 90 VAL cc_start: 0.8981 (t) cc_final: 0.8747 (t) REVERT: 2E 66 HIS cc_start: 0.8294 (m-70) cc_final: 0.7948 (m170) REVERT: 2G 64 MET cc_start: 0.8608 (ttm) cc_final: 0.8308 (ttp) REVERT: 2H 64 MET cc_start: 0.8481 (ttm) cc_final: 0.8254 (ttp) REVERT: 3A 57 MET cc_start: 0.7051 (ttp) cc_final: 0.6845 (ttm) REVERT: 3H 30 THR cc_start: 0.9001 (p) cc_final: 0.8748 (p) REVERT: 3J 64 MET cc_start: 0.8590 (ttm) cc_final: 0.8375 (ttp) REVERT: 4A 62 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7796 (mmm) REVERT: 4J 62 MET cc_start: 0.8573 (mmp) cc_final: 0.8278 (mmt) REVERT: 4K 64 MET cc_start: 0.8697 (ttm) cc_final: 0.8449 (ttp) REVERT: 5C 30 THR cc_start: 0.8863 (p) cc_final: 0.8546 (p) REVERT: 5H 62 MET cc_start: 0.8593 (mmp) cc_final: 0.8362 (mmp) outliers start: 25 outliers final: 2 residues processed: 587 average time/residue: 1.2407 time to fit residues: 927.6122 Evaluate side-chains 474 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 471 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4A residue 62 MET Chi-restraints excluded: chain 4B residue 73 ILE Chi-restraints excluded: chain 5B residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 247 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 370 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 445 optimal weight: 0.0980 chunk 481 optimal weight: 4.9990 chunk 397 optimal weight: 6.9990 chunk 442 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1C 66 HIS 4C 66 HIS ** 5B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 40040 Z= 0.237 Angle : 0.499 5.652 53970 Z= 0.248 Chirality : 0.041 0.135 6510 Planarity : 0.004 0.035 6020 Dihedral : 23.794 89.954 8260 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.40 % Allowed : 7.14 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.13), residues: 4760 helix: 3.30 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.39 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP4D 47 HIS 0.010 0.001 HIS5B 66 PHE 0.009 0.001 PHE2J 61 TYR 0.007 0.001 TYR1M 88 ARG 0.010 0.001 ARG3A 75 *********************** 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 586 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 530 time to evaluate : 4.259 Fit side-chains REVERT: 2H 64 MET cc_start: 0.8645 (ttm) cc_final: 0.8398 (ttp) REVERT: 3D 75 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8071 (ttp-170) REVERT: 3H 30 THR cc_start: 0.8952 (p) cc_final: 0.8726 (p) REVERT: 3J 64 MET cc_start: 0.8669 (ttm) cc_final: 0.8463 (ttp) REVERT: 3N 88 TYR cc_start: 0.9021 (t80) cc_final: 0.8738 (t80) REVERT: 4A 62 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7891 (mmm) REVERT: 4C 71 SER cc_start: 0.8939 (p) cc_final: 0.8467 (m) REVERT: 4J 62 MET cc_start: 0.8819 (mmp) cc_final: 0.8480 (mmp) REVERT: 4K 64 MET cc_start: 0.8723 (ttp) cc_final: 0.8512 (ttp) REVERT: 5H 62 MET cc_start: 0.8647 (mmp) cc_final: 0.8395 (mmp) outliers start: 56 outliers final: 36 residues processed: 567 average time/residue: 1.1849 time to fit residues: 860.0550 Evaluate side-chains 528 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 490 time to evaluate : 5.459 ------------------------------------------------------------------------------- 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 2B residue 59 SER 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 3D residue 75 ARG 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 4B residue 59 SER 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 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 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 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 440 optimal weight: 1.9990 chunk 335 optimal weight: 0.8980 chunk 231 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 212 optimal weight: 8.9990 chunk 299 optimal weight: 7.9990 chunk 447 optimal weight: 4.9990 chunk 473 optimal weight: 0.4980 chunk 233 optimal weight: 4.9990 chunk 424 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 66 HIS 1F 66 HIS 1G 66 HIS 4C 66 HIS 5E 66 HIS 5G 66 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 40040 Z= 0.192 Angle : 0.476 5.368 53970 Z= 0.231 Chirality : 0.041 0.129 6510 Planarity : 0.004 0.030 6020 Dihedral : 20.719 81.507 8260 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.75 % Allowed : 9.00 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.12), residues: 4760 helix: 3.35 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.43 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP1F 47 HIS 0.005 0.001 HIS1B 66 PHE 0.004 0.001 PHE2J 61 TYR 0.007 0.001 TYR5N 88 ARG 0.005 0.001 ARG2J 75 *********************** 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 556 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 526 time to evaluate : 4.448 Fit side-chains REVERT: 2A 75 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7194 (ttp80) REVERT: 2C 71 SER cc_start: 0.8795 (p) cc_final: 0.8560 (m) REVERT: 2D 75 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7434 (ttm170) REVERT: 2M 71 SER cc_start: 0.9032 (p) cc_final: 0.8828 (m) REVERT: 3H 30 THR cc_start: 0.8906 (p) cc_final: 0.8702 (p) REVERT: 3N 88 TYR cc_start: 0.9018 (t80) cc_final: 0.8733 (t80) REVERT: 4C 71 SER cc_start: 0.8905 (p) cc_final: 0.8502 (m) REVERT: 4C 90 VAL cc_start: 0.8691 (t) cc_final: 0.8401 (t) REVERT: 4J 62 MET cc_start: 0.8780 (mmp) cc_final: 0.8491 (mmp) REVERT: 5H 62 MET cc_start: 0.8628 (mmp) cc_final: 0.8397 (mmp) REVERT: 5M 71 SER cc_start: 0.8904 (p) cc_final: 0.8694 (m) outliers start: 30 outliers final: 15 residues processed: 545 average time/residue: 1.2444 time to fit residues: 862.2792 Evaluate side-chains 520 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 503 time to evaluate : 4.415 ------------------------------------------------------------------------------- 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 59 SER Chi-restraints excluded: chain 2D residue 75 ARG Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4I 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 394 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 352 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 404 optimal weight: 7.9990 chunk 327 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 241 optimal weight: 8.9990 chunk 425 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1F 66 HIS 1G 66 HIS 2A 41 GLN 2H 66 HIS ** 3B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3L 66 HIS 4C 66 HIS 4D 66 HIS 4G 66 HIS 5C 66 HIS 5E 66 HIS 5G 66 HIS 5I 66 HIS 5L 66 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 40040 Z= 0.262 Angle : 0.529 6.617 53970 Z= 0.257 Chirality : 0.043 0.139 6510 Planarity : 0.004 0.029 6020 Dihedral : 19.185 82.502 8260 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.10 % Allowed : 9.05 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.12), residues: 4760 helix: 3.26 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.58 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP4D 47 HIS 0.005 0.001 HIS5I 66 PHE 0.006 0.001 PHE2J 61 TYR 0.008 0.001 TYR5N 88 ARG 0.006 0.001 ARG3F 75 *********************** 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 556 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 512 time to evaluate : 4.697 Fit side-chains revert: symmetry clash REVERT: 1N 64 MET cc_start: 0.9161 (ttp) cc_final: 0.8910 (ttm) REVERT: 2A 75 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7115 (ttp80) REVERT: 2B 75 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7355 (ttm110) REVERT: 2C 71 SER cc_start: 0.8960 (p) cc_final: 0.8650 (m) REVERT: 2K 31 ASP cc_start: 0.8681 (t0) cc_final: 0.8466 (t0) REVERT: 2M 71 SER cc_start: 0.9077 (p) cc_final: 0.8854 (m) REVERT: 3N 88 TYR cc_start: 0.9043 (t80) cc_final: 0.8737 (t80) REVERT: 4C 71 SER cc_start: 0.8970 (p) cc_final: 0.8589 (m) REVERT: 4C 90 VAL cc_start: 0.8772 (t) cc_final: 0.8468 (t) REVERT: 4J 62 MET cc_start: 0.8818 (mmp) cc_final: 0.8586 (mmp) REVERT: 5C 71 SER cc_start: 0.9009 (p) cc_final: 0.8685 (m) outliers start: 44 outliers final: 28 residues processed: 547 average time/residue: 1.2321 time to fit residues: 859.8840 Evaluate side-chains 518 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 488 time to evaluate : 4.528 ------------------------------------------------------------------------------- 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 2B residue 75 ARG 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 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 4E residue 91 SER Chi-restraints excluded: chain 4F residue 91 SER Chi-restraints excluded: chain 4G 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 64 MET Chi-restraints excluded: chain 5E residue 91 SER Chi-restraints excluded: chain 5F residue 91 SER Chi-restraints excluded: chain 5I residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 0.9990 chunk 426 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 278 optimal weight: 0.9990 chunk 116 optimal weight: 0.0050 chunk 474 optimal weight: 6.9990 chunk 393 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 39 optimal weight: 0.0170 chunk 156 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 overall best weight: 1.0038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1B 66 HIS 1F 66 HIS 2A 41 GLN 2H 66 HIS 3A 41 GLN 3B 66 HIS 4C 66 HIS 4D 66 HIS 4G 66 HIS 5G 66 HIS 5I 66 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2737 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= 0.145 Angle : 0.429 6.188 53970 Z= 0.211 Chirality : 0.040 0.119 6510 Planarity : 0.004 0.030 6020 Dihedral : 18.183 83.208 8260 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.95 % Allowed : 9.35 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.12), residues: 4760 helix: 3.49 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.49 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP5L 47 HIS 0.004 0.001 HIS1B 66 PHE 0.003 0.001 PHE2J 72 TYR 0.006 0.001 TYR5D 88 ARG 0.003 0.000 ARG3J 75 *********************** 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 578 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 540 time to evaluate : 4.259 Fit side-chains REVERT: 2A 75 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7216 (ttp80) REVERT: 2B 75 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7305 (ttm110) REVERT: 2C 71 SER cc_start: 0.8853 (p) cc_final: 0.8577 (m) REVERT: 2D 75 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7398 (ttm170) REVERT: 3A 75 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8043 (ttp80) REVERT: 3C 71 SER cc_start: 0.8855 (p) cc_final: 0.8567 (m) REVERT: 3N 88 TYR cc_start: 0.9035 (t80) cc_final: 0.8717 (t80) REVERT: 4A 64 MET cc_start: 0.7138 (ttm) cc_final: 0.6813 (ttp) REVERT: 4A 75 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6498 (ttm170) REVERT: 4C 71 SER cc_start: 0.8835 (p) cc_final: 0.8503 (m) REVERT: 4C 90 VAL cc_start: 0.8658 (t) cc_final: 0.8435 (t) REVERT: 4J 62 MET cc_start: 0.8694 (mmp) cc_final: 0.8450 (mmp) outliers start: 38 outliers final: 15 residues processed: 562 average time/residue: 1.2581 time to fit residues: 907.9044 Evaluate side-chains 536 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 516 time to evaluate : 4.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1C residue 91 SER Chi-restraints excluded: chain 1D residue 91 SER Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2B residue 75 ARG Chi-restraints excluded: chain 2D residue 75 ARG Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 3A residue 75 ARG Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3G residue 91 SER Chi-restraints excluded: chain 3L residue 64 MET Chi-restraints excluded: chain 4A residue 75 ARG Chi-restraints excluded: chain 4D residue 91 SER Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4F residue 91 SER Chi-restraints excluded: chain 4J residue 91 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5D residue 91 SER Chi-restraints excluded: chain 5F residue 91 SER Chi-restraints excluded: chain 5J residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 457 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 346 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 chunk 399 optimal weight: 0.0000 chunk 264 optimal weight: 5.9990 chunk 472 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 287 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- 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 1F 66 HIS 1G 66 HIS 2A 41 GLN 2E 66 HIS 2H 66 HIS 3A 41 GLN 4C 66 HIS 5G 66 HIS 5I 66 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 40040 Z= 0.199 Angle : 0.468 6.546 53970 Z= 0.229 Chirality : 0.041 0.125 6510 Planarity : 0.004 0.028 6020 Dihedral : 18.131 80.699 8260 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.95 % Allowed : 9.67 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.01 (0.12), residues: 4760 helix: 3.42 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.52 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP1F 47 HIS 0.005 0.001 HIS1B 66 PHE 0.004 0.001 PHE2J 61 TYR 0.008 0.001 TYR5D 88 ARG 0.004 0.001 ARG3J 75 *********************** 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 558 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 520 time to evaluate : 4.222 Fit side-chains revert: symmetry clash REVERT: 1C 71 SER cc_start: 0.8826 (p) cc_final: 0.8569 (m) REVERT: 2A 75 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7183 (ttp80) REVERT: 2B 75 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7300 (ttm110) REVERT: 2C 71 SER cc_start: 0.8891 (p) cc_final: 0.8614 (m) REVERT: 3C 71 SER cc_start: 0.8896 (p) cc_final: 0.8595 (m) REVERT: 3N 88 TYR cc_start: 0.9037 (t80) cc_final: 0.8736 (t80) REVERT: 4A 64 MET cc_start: 0.7226 (ttm) cc_final: 0.6895 (ttp) REVERT: 4C 71 SER cc_start: 0.8856 (p) cc_final: 0.8525 (m) REVERT: 4C 90 VAL cc_start: 0.8722 (t) cc_final: 0.8452 (t) REVERT: 4J 62 MET cc_start: 0.8785 (mmp) cc_final: 0.8562 (mmp) REVERT: 5N 34 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7581 (tm-30) outliers start: 38 outliers final: 23 residues processed: 546 average time/residue: 1.2595 time to fit residues: 872.0643 Evaluate side-chains 528 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 503 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 75 ARG 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 64 MET Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2B residue 75 ARG Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3B residue 91 SER 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 4E residue 91 SER Chi-restraints excluded: chain 4F residue 91 SER Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 4J residue 91 SER Chi-restraints excluded: chain 5B residue 48 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 292 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 282 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 300 optimal weight: 0.0050 chunk 321 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 371 optimal weight: 0.8980 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1B 66 HIS 1F 66 HIS 1G 66 HIS 2A 41 GLN 2H 66 HIS 3A 41 GLN 4G 66 HIS 5G 66 HIS 5I 66 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2821 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= 0.161 Angle : 0.439 6.490 53970 Z= 0.215 Chirality : 0.041 0.119 6510 Planarity : 0.004 0.028 6020 Dihedral : 17.808 81.075 8260 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.80 % Allowed : 9.87 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.12), residues: 4760 helix: 3.49 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.45 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP5D 47 HIS 0.004 0.001 HIS1B 66 PHE 0.003 0.001 PHE2J 61 TYR 0.007 0.001 TYR5D 88 ARG 0.002 0.000 ARG2H 75 *********************** 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 556 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 524 time to evaluate : 4.374 Fit side-chains REVERT: 1C 71 SER cc_start: 0.8750 (p) cc_final: 0.8514 (m) REVERT: 2A 75 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7216 (ttp80) REVERT: 2B 75 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7300 (ttm110) REVERT: 2C 71 SER cc_start: 0.8887 (p) cc_final: 0.8615 (m) REVERT: 3C 71 SER cc_start: 0.8805 (p) cc_final: 0.8549 (m) REVERT: 3L 64 MET cc_start: 0.8749 (ttp) cc_final: 0.8354 (ttm) REVERT: 3N 88 TYR cc_start: 0.9040 (t80) cc_final: 0.8700 (t80) REVERT: 4A 64 MET cc_start: 0.7233 (ttm) cc_final: 0.6899 (ttp) REVERT: 4A 75 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6555 (ttm170) REVERT: 4B 75 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7880 (ttm110) REVERT: 4C 71 SER cc_start: 0.8829 (p) cc_final: 0.8511 (m) REVERT: 4C 90 VAL cc_start: 0.8696 (t) cc_final: 0.8440 (t) REVERT: 4J 62 MET cc_start: 0.8692 (mmp) cc_final: 0.8461 (mmp) REVERT: 5K 71 SER cc_start: 0.8842 (p) cc_final: 0.8538 (m) REVERT: 5L 71 SER cc_start: 0.9137 (p) cc_final: 0.8900 (m) REVERT: 5N 34 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7571 (tm-30) outliers start: 32 outliers final: 25 residues processed: 550 average time/residue: 1.2348 time to fit residues: 863.1144 Evaluate side-chains 534 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 506 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1H residue 64 MET Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2B residue 75 ARG Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3A residue 64 MET 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 4A residue 75 ARG Chi-restraints excluded: chain 4A residue 76 ILE 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 4J residue 91 SER Chi-restraints excluded: chain 5B residue 48 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 429 optimal weight: 2.9990 chunk 452 optimal weight: 0.1980 chunk 412 optimal weight: 0.9980 chunk 440 optimal weight: 1.9990 chunk 264 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 345 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 397 optimal weight: 0.9980 chunk 416 optimal weight: 6.9990 chunk 438 optimal weight: 0.0370 overall best weight: 0.6460 ------------------------------------------------------------------------------- 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 2E 66 HIS 2H 66 HIS 3A 41 GLN 4C 66 HIS 4I 66 HIS 5I 66 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 40040 Z= 0.127 Angle : 0.416 6.697 53970 Z= 0.201 Chirality : 0.040 0.120 6510 Planarity : 0.004 0.028 6020 Dihedral : 17.272 81.482 8260 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.70 % Allowed : 10.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.29 (0.12), residues: 4760 helix: 3.59 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.31 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP5I 47 HIS 0.003 0.001 HIS5B 66 PHE 0.003 0.001 PHE4J 61 TYR 0.008 0.000 TYR1B 88 ARG 0.002 0.000 ARG1A 75 *********************** 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 577 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 549 time to evaluate : 4.530 Fit side-chains REVERT: 2A 75 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7303 (ttp80) REVERT: 2C 71 SER cc_start: 0.8904 (p) cc_final: 0.8570 (m) REVERT: 3B 41 GLN cc_start: 0.9168 (tt0) cc_final: 0.8947 (tt0) REVERT: 3C 71 SER cc_start: 0.8686 (p) cc_final: 0.8446 (m) REVERT: 3D 57 MET cc_start: 0.8518 (ttp) cc_final: 0.8290 (ttp) REVERT: 3M 71 SER cc_start: 0.8797 (p) cc_final: 0.8514 (m) REVERT: 3N 88 TYR cc_start: 0.8995 (t80) cc_final: 0.8648 (t80) REVERT: 4A 42 THR cc_start: 0.8951 (m) cc_final: 0.8711 (p) REVERT: 4A 64 MET cc_start: 0.7188 (ttm) cc_final: 0.6863 (ttp) REVERT: 4A 75 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6418 (ttm170) REVERT: 4B 75 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7688 (ttm110) REVERT: 4C 90 VAL cc_start: 0.8595 (t) cc_final: 0.8395 (t) REVERT: 5I 71 SER cc_start: 0.8588 (p) cc_final: 0.8310 (m) REVERT: 5K 71 SER cc_start: 0.8697 (p) cc_final: 0.8439 (m) REVERT: 5N 59 SER cc_start: 0.9258 (m) cc_final: 0.8971 (m) outliers start: 28 outliers final: 18 residues processed: 572 average time/residue: 1.1977 time to fit residues: 881.9225 Evaluate side-chains 538 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 518 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 64 MET Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2D residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 3A residue 64 MET 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 4A residue 30 THR Chi-restraints excluded: chain 4A residue 75 ARG Chi-restraints excluded: chain 4G residue 91 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 5.9990 chunk 465 optimal weight: 5.9990 chunk 284 optimal weight: 0.6980 chunk 220 optimal weight: 4.9990 chunk 323 optimal weight: 0.9980 chunk 488 optimal weight: 2.9990 chunk 449 optimal weight: 0.9980 chunk 388 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 300 optimal weight: 0.0070 chunk 238 optimal weight: 10.0000 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 2E 66 HIS 2H 66 HIS 3A 41 GLN 4C 66 HIS 4I 66 HIS 5E 66 HIS 5I 66 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 40040 Z= 0.149 Angle : 0.435 7.569 53970 Z= 0.210 Chirality : 0.040 0.119 6510 Planarity : 0.004 0.029 6020 Dihedral : 17.243 81.736 8260 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.53 % Allowed : 10.30 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.25 (0.12), residues: 4760 helix: 3.57 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.35 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP1F 47 HIS 0.006 0.001 HIS1B 66 PHE 0.003 0.001 PHE5M 72 TYR 0.006 0.000 TYR2K 88 ARG 0.003 0.000 ARG3F 75 ********************** 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: 21 poor density : 516 time to evaluate : 5.201 Fit side-chains REVERT: 2A 75 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7295 (ttp80) REVERT: 2B 75 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7244 (ttm110) REVERT: 2C 71 SER cc_start: 0.8847 (p) cc_final: 0.8586 (m) REVERT: 3C 71 SER cc_start: 0.8725 (p) cc_final: 0.8480 (m) REVERT: 3D 57 MET cc_start: 0.8554 (ttp) cc_final: 0.8330 (ttp) REVERT: 3M 71 SER cc_start: 0.8830 (p) cc_final: 0.8562 (m) REVERT: 3M 90 VAL cc_start: 0.8953 (t) cc_final: 0.8696 (t) REVERT: 3N 88 TYR cc_start: 0.8995 (t80) cc_final: 0.8665 (t80) REVERT: 4A 42 THR cc_start: 0.8931 (m) cc_final: 0.8679 (p) REVERT: 4A 64 MET cc_start: 0.7389 (ttm) cc_final: 0.7061 (ttp) REVERT: 4A 75 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6499 (ttm170) REVERT: 4B 75 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7806 (ttm110) REVERT: 4C 90 VAL cc_start: 0.8688 (t) cc_final: 0.8443 (t) REVERT: 4J 62 MET cc_start: 0.8685 (mmp) cc_final: 0.8403 (mmp) REVERT: 4K 64 MET cc_start: 0.8842 (ttm) cc_final: 0.8593 (ttp) REVERT: 5I 71 SER cc_start: 0.8651 (p) cc_final: 0.8354 (m) REVERT: 5K 71 SER cc_start: 0.8734 (p) cc_final: 0.8498 (m) REVERT: 5N 59 SER cc_start: 0.9267 (m) cc_final: 0.9031 (m) outliers start: 21 outliers final: 17 residues processed: 531 average time/residue: 1.2622 time to fit residues: 855.0280 Evaluate side-chains 529 residues out of total 3990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 509 time to evaluate : 4.255 ------------------------------------------------------------------------------- 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 30 THR 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 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 64 MET Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3G residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4A residue 75 ARG Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5E residue 91 SER Chi-restraints excluded: chain 5F residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 308 optimal weight: 9.9990 chunk 414 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 358 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 389 optimal weight: 0.9980 chunk 162 optimal weight: 0.9990 chunk 399 optimal weight: 0.0030 chunk 49 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- 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 2E 66 HIS 2H 66 HIS 3A 41 GLN 4C 66 HIS 4I 66 HIS 5E 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 = 0.3209 r_free = 0.3209 target = 0.104479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.077422 restraints weight = 45228.874| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 1.53 r_work: 0.2683 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3067 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= 0.141 Angle : 0.432 8.397 53970 Z= 0.208 Chirality : 0.040 0.119 6510 Planarity : 0.004 0.034 6020 Dihedral : 17.165 82.105 8260 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.70 % Allowed : 10.13 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.12), residues: 4760 helix: 3.56 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.36 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP4H 47 HIS 0.007 0.001 HIS1B 66 PHE 0.003 0.001 PHE4M 72 TYR 0.004 0.000 TYR5N 88 ARG 0.003 0.000 ARG3F 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12570.14 seconds wall clock time: 230 minutes 11.62 seconds (13811.62 seconds total)