Starting phenix.real_space_refine on Sat Mar 7 03:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cue_26999/03_2026/8cue_26999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cue_26999/03_2026/8cue_26999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cue_26999/03_2026/8cue_26999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cue_26999/03_2026/8cue_26999.map" model { file = "/net/cci-nas-00/data/ceres_data/8cue_26999/03_2026/8cue_26999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cue_26999/03_2026/8cue_26999.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.135 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 280 5.16 5 C 24920 2.51 5 N 5530 2.21 5 O 6440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37240 Number of models: 1 Model: "" Number of chains: 140 Chain: "1A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.92, per 1000 atoms: 0.21 Number of scatterers: 37240 At special positions: 0 Unit cell: (94.83, 94.83, 243.07, 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 280 16.00 P 70 15.00 O 6440 8.00 N 5530 7.00 C 24920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.6 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: 7560 Finding SS restraints... Secondary structure from input PDB file: 280 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain '1A' and resid 55 through 68 removed outlier: 3.603A pdb=" N MET1A 59 " --> pdb=" O ASP1A 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1A 61 " --> pdb=" O ALA1A 57 " (cutoff:3.500A) Processing helix chain '1A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1A 77 " --> pdb=" O GLN1A 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU1A 78 " --> pdb=" O SER1A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1A 83 " --> pdb=" O GLY1A 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1A 88 " --> pdb=" O GLY1A 84 " (cutoff:3.500A) Processing helix chain '1A' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1A 97 " --> pdb=" O SER1A 93 " (cutoff:3.500A) Processing helix chain '1A' and resid 109 through 119 removed outlier: 3.543A pdb=" N LEU1A 113 " --> pdb=" O GLY1A 109 " (cutoff:3.500A) Processing helix chain '1B' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1B 59 " --> pdb=" O ASP1B 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1B 61 " --> pdb=" O ALA1B 57 " (cutoff:3.500A) Processing helix chain '1B' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL1B 77 " --> pdb=" O GLN1B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1B 78 " --> pdb=" O SER1B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1B 83 " --> pdb=" O GLY1B 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1B 88 " --> pdb=" O GLY1B 84 " (cutoff:3.500A) Processing helix chain '1B' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1B 97 " --> pdb=" O SER1B 93 " (cutoff:3.500A) Processing helix chain '1B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1B 113 " --> pdb=" O GLY1B 109 " (cutoff:3.500A) Processing helix chain '1C' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1C 59 " --> pdb=" O ASP1C 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1C 61 " --> pdb=" O ALA1C 57 " (cutoff:3.500A) Processing helix chain '1C' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1C 77 " --> pdb=" O GLN1C 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1C 78 " --> pdb=" O SER1C 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1C 83 " --> pdb=" O GLY1C 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1C 88 " --> pdb=" O GLY1C 84 " (cutoff:3.500A) Processing helix chain '1C' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1C 97 " --> pdb=" O SER1C 93 " (cutoff:3.500A) Processing helix chain '1C' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1C 113 " --> pdb=" O GLY1C 109 " (cutoff:3.500A) Processing helix chain '1D' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1D 59 " --> pdb=" O ASP1D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1D 61 " --> pdb=" O ALA1D 57 " (cutoff:3.500A) Processing helix chain '1D' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL1D 77 " --> pdb=" O GLN1D 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU1D 78 " --> pdb=" O SER1D 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE1D 83 " --> pdb=" O GLY1D 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET1D 88 " --> pdb=" O GLY1D 84 " (cutoff:3.500A) Processing helix chain '1D' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1D 97 " --> pdb=" O SER1D 93 " (cutoff:3.500A) Processing helix chain '1D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1D 113 " --> pdb=" O GLY1D 109 " (cutoff:3.500A) Processing helix chain '1E' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1E 59 " --> pdb=" O ASP1E 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1E 61 " --> pdb=" O ALA1E 57 " (cutoff:3.500A) Processing helix chain '1E' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1E 77 " --> pdb=" O GLN1E 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1E 78 " --> pdb=" O SER1E 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1E 83 " --> pdb=" O GLY1E 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET1E 88 " --> pdb=" O GLY1E 84 " (cutoff:3.500A) Processing helix chain '1E' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1E 97 " --> pdb=" O SER1E 93 " (cutoff:3.500A) Processing helix chain '1E' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1E 113 " --> pdb=" O GLY1E 109 " (cutoff:3.500A) Processing helix chain '1F' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1F 59 " --> pdb=" O ASP1F 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1F 61 " --> pdb=" O ALA1F 57 " (cutoff:3.500A) Processing helix chain '1F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1F 77 " --> pdb=" O GLN1F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1F 78 " --> pdb=" O SER1F 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1F 83 " --> pdb=" O GLY1F 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1F 88 " --> pdb=" O GLY1F 84 " (cutoff:3.500A) Processing helix chain '1F' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1F 97 " --> pdb=" O SER1F 93 " (cutoff:3.500A) Processing helix chain '1F' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU1F 113 " --> pdb=" O GLY1F 109 " (cutoff:3.500A) Processing helix chain '1G' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1G 59 " --> pdb=" O ASP1G 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN1G 61 " --> pdb=" O ALA1G 57 " (cutoff:3.500A) Processing helix chain '1G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1G 77 " --> pdb=" O GLN1G 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1G 78 " --> pdb=" O SER1G 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1G 83 " --> pdb=" O GLY1G 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1G 88 " --> pdb=" O GLY1G 84 " (cutoff:3.500A) Processing helix chain '1G' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1G 97 " --> pdb=" O SER1G 93 " (cutoff:3.500A) Processing helix chain '1G' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1G 113 " --> pdb=" O GLY1G 109 " (cutoff:3.500A) Processing helix chain '1H' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1H 59 " --> pdb=" O ASP1H 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN1H 61 " --> pdb=" O ALA1H 57 " (cutoff:3.500A) Processing helix chain '1H' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1H 77 " --> pdb=" O GLN1H 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1H 78 " --> pdb=" O SER1H 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1H 83 " --> pdb=" O GLY1H 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1H 88 " --> pdb=" O GLY1H 84 " (cutoff:3.500A) Processing helix chain '1H' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1H 97 " --> pdb=" O SER1H 93 " (cutoff:3.500A) Processing helix chain '1H' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1H 113 " --> pdb=" O GLY1H 109 " (cutoff:3.500A) Processing helix chain '1I' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1I 59 " --> pdb=" O ASP1I 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1I 61 " --> pdb=" O ALA1I 57 " (cutoff:3.500A) Processing helix chain '1I' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL1I 77 " --> pdb=" O GLN1I 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1I 78 " --> pdb=" O SER1I 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE1I 83 " --> pdb=" O GLY1I 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1I 88 " --> pdb=" O GLY1I 84 " (cutoff:3.500A) Processing helix chain '1I' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1I 97 " --> pdb=" O SER1I 93 " (cutoff:3.500A) Processing helix chain '1I' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1I 113 " --> pdb=" O GLY1I 109 " (cutoff:3.500A) Processing helix chain '1J' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1J 59 " --> pdb=" O ASP1J 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN1J 61 " --> pdb=" O ALA1J 57 " (cutoff:3.500A) Processing helix chain '1J' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1J 77 " --> pdb=" O GLN1J 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1J 78 " --> pdb=" O SER1J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1J 83 " --> pdb=" O GLY1J 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1J 88 " --> pdb=" O GLY1J 84 " (cutoff:3.500A) Processing helix chain '1J' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1J 97 " --> pdb=" O SER1J 93 " (cutoff:3.500A) Processing helix chain '1J' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1J 113 " --> pdb=" O GLY1J 109 " (cutoff:3.500A) Processing helix chain '1K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1K 59 " --> pdb=" O ASP1K 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN1K 61 " --> pdb=" O ALA1K 57 " (cutoff:3.500A) Processing helix chain '1K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1K 77 " --> pdb=" O GLN1K 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1K 78 " --> pdb=" O SER1K 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1K 83 " --> pdb=" O GLY1K 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET1K 88 " --> pdb=" O GLY1K 84 " (cutoff:3.500A) Processing helix chain '1K' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1K 97 " --> pdb=" O SER1K 93 " (cutoff:3.500A) Processing helix chain '1K' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1K 113 " --> pdb=" O GLY1K 109 " (cutoff:3.500A) Processing helix chain '1L' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1L 59 " --> pdb=" O ASP1L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1L 61 " --> pdb=" O ALA1L 57 " (cutoff:3.500A) Processing helix chain '1L' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1L 77 " --> pdb=" O GLN1L 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1L 78 " --> pdb=" O SER1L 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1L 83 " --> pdb=" O GLY1L 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1L 88 " --> pdb=" O GLY1L 84 " (cutoff:3.500A) Processing helix chain '1L' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1L 97 " --> pdb=" O SER1L 93 " (cutoff:3.500A) Processing helix chain '1L' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1L 113 " --> pdb=" O GLY1L 109 " (cutoff:3.500A) Processing helix chain '1M' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1M 59 " --> pdb=" O ASP1M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1M 61 " --> pdb=" O ALA1M 57 " (cutoff:3.500A) Processing helix chain '1M' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1M 77 " --> pdb=" O GLN1M 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1M 78 " --> pdb=" O SER1M 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1M 83 " --> pdb=" O GLY1M 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1M 88 " --> pdb=" O GLY1M 84 " (cutoff:3.500A) Processing helix chain '1M' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1M 97 " --> pdb=" O SER1M 93 " (cutoff:3.500A) Processing helix chain '1M' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU1M 113 " --> pdb=" O GLY1M 109 " (cutoff:3.500A) Processing helix chain '1N' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1N 59 " --> pdb=" O ASP1N 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1N 61 " --> pdb=" O ALA1N 57 " (cutoff:3.500A) Processing helix chain '1N' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1N 77 " --> pdb=" O GLN1N 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1N 78 " --> pdb=" O SER1N 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1N 83 " --> pdb=" O GLY1N 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1N 88 " --> pdb=" O GLY1N 84 " (cutoff:3.500A) Processing helix chain '1N' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1N 97 " --> pdb=" O SER1N 93 " (cutoff:3.500A) Processing helix chain '1N' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1N 113 " --> pdb=" O GLY1N 109 " (cutoff:3.500A) Processing helix chain '2A' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2A 59 " --> pdb=" O ASP2A 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2A 61 " --> pdb=" O ALA2A 57 " (cutoff:3.500A) Processing helix chain '2A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2A 77 " --> pdb=" O GLN2A 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2A 78 " --> pdb=" O SER2A 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE2A 83 " --> pdb=" O GLY2A 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2A 88 " --> pdb=" O GLY2A 84 " (cutoff:3.500A) Processing helix chain '2A' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2A 97 " --> pdb=" O SER2A 93 " (cutoff:3.500A) Processing helix chain '2A' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2A 113 " --> pdb=" O GLY2A 109 " (cutoff:3.500A) Processing helix chain '2B' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET2B 59 " --> pdb=" O ASP2B 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN2B 61 " --> pdb=" O ALA2B 57 " (cutoff:3.500A) Processing helix chain '2B' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2B 77 " --> pdb=" O GLN2B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2B 78 " --> pdb=" O SER2B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2B 83 " --> pdb=" O GLY2B 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET2B 88 " --> pdb=" O GLY2B 84 " (cutoff:3.500A) Processing helix chain '2B' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL2B 97 " --> pdb=" O SER2B 93 " (cutoff:3.500A) Processing helix chain '2B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2B 113 " --> pdb=" O GLY2B 109 " (cutoff:3.500A) Processing helix chain '2C' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2C 59 " --> pdb=" O ASP2C 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2C 61 " --> pdb=" O ALA2C 57 " (cutoff:3.500A) Processing helix chain '2C' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2C 77 " --> pdb=" O GLN2C 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2C 78 " --> pdb=" O SER2C 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2C 83 " --> pdb=" O GLY2C 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2C 88 " --> pdb=" O GLY2C 84 " (cutoff:3.500A) Processing helix chain '2C' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2C 97 " --> pdb=" O SER2C 93 " (cutoff:3.500A) Processing helix chain '2C' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU2C 113 " --> pdb=" O GLY2C 109 " (cutoff:3.500A) Processing helix chain '2D' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET2D 59 " --> pdb=" O ASP2D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2D 61 " --> pdb=" O ALA2D 57 " (cutoff:3.500A) Processing helix chain '2D' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2D 77 " --> pdb=" O GLN2D 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2D 78 " --> pdb=" O SER2D 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2D 83 " --> pdb=" O GLY2D 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2D 88 " --> pdb=" O GLY2D 84 " (cutoff:3.500A) Processing helix chain '2D' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2D 97 " --> pdb=" O SER2D 93 " (cutoff:3.500A) Processing helix chain '2D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2D 113 " --> pdb=" O GLY2D 109 " (cutoff:3.500A) Processing helix chain '2E' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2E 59 " --> pdb=" O ASP2E 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN2E 61 " --> pdb=" O ALA2E 57 " (cutoff:3.500A) Processing helix chain '2E' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL2E 77 " --> pdb=" O GLN2E 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2E 78 " --> pdb=" O SER2E 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2E 83 " --> pdb=" O GLY2E 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2E 88 " --> pdb=" O GLY2E 84 " (cutoff:3.500A) Processing helix chain '2E' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2E 97 " --> pdb=" O SER2E 93 " (cutoff:3.500A) Processing helix chain '2E' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2E 113 " --> pdb=" O GLY2E 109 " (cutoff:3.500A) Processing helix chain '2F' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2F 59 " --> pdb=" O ASP2F 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN2F 61 " --> pdb=" O ALA2F 57 " (cutoff:3.500A) Processing helix chain '2F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2F 77 " --> pdb=" O GLN2F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2F 78 " --> pdb=" O SER2F 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE2F 83 " --> pdb=" O GLY2F 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET2F 88 " --> pdb=" O GLY2F 84 " (cutoff:3.500A) Processing helix chain '2F' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2F 97 " --> pdb=" O SER2F 93 " (cutoff:3.500A) Processing helix chain '2F' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU2F 113 " --> pdb=" O GLY2F 109 " (cutoff:3.500A) Processing helix chain '2G' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2G 59 " --> pdb=" O ASP2G 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN2G 61 " --> pdb=" O ALA2G 57 " (cutoff:3.500A) Processing helix chain '2G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2G 77 " --> pdb=" O GLN2G 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU2G 78 " --> pdb=" O SER2G 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2G 83 " --> pdb=" O GLY2G 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2G 88 " --> pdb=" O GLY2G 84 " (cutoff:3.500A) Processing helix chain '2G' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL2G 97 " --> pdb=" O SER2G 93 " (cutoff:3.500A) Processing helix chain '2G' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2G 113 " --> pdb=" O GLY2G 109 " (cutoff:3.500A) Processing helix chain '2H' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2H 59 " --> pdb=" O ASP2H 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2H 61 " --> pdb=" O ALA2H 57 " (cutoff:3.500A) Processing helix chain '2H' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2H 77 " --> pdb=" O GLN2H 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2H 78 " --> pdb=" O SER2H 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2H 83 " --> pdb=" O GLY2H 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET2H 88 " --> pdb=" O GLY2H 84 " (cutoff:3.500A) Processing helix chain '2H' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2H 97 " --> pdb=" O SER2H 93 " (cutoff:3.500A) Processing helix chain '2H' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2H 113 " --> pdb=" O GLY2H 109 " (cutoff:3.500A) Processing helix chain '2I' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET2I 59 " --> pdb=" O ASP2I 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2I 61 " --> pdb=" O ALA2I 57 " (cutoff:3.500A) Processing helix chain '2I' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL2I 77 " --> pdb=" O GLN2I 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2I 78 " --> pdb=" O SER2I 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2I 83 " --> pdb=" O GLY2I 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2I 88 " --> pdb=" O GLY2I 84 " (cutoff:3.500A) Processing helix chain '2I' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2I 97 " --> pdb=" O SER2I 93 " (cutoff:3.500A) Processing helix chain '2I' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2I 113 " --> pdb=" O GLY2I 109 " (cutoff:3.500A) Processing helix chain '2J' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2J 59 " --> pdb=" O ASP2J 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2J 61 " --> pdb=" O ALA2J 57 " (cutoff:3.500A) Processing helix chain '2J' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2J 77 " --> pdb=" O GLN2J 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2J 78 " --> pdb=" O SER2J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2J 83 " --> pdb=" O GLY2J 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2J 88 " --> pdb=" O GLY2J 84 " (cutoff:3.500A) Processing helix chain '2J' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2J 97 " --> pdb=" O SER2J 93 " (cutoff:3.500A) Processing helix chain '2J' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2J 113 " --> pdb=" O GLY2J 109 " (cutoff:3.500A) Processing helix chain '2K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2K 59 " --> pdb=" O ASP2K 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2K 61 " --> pdb=" O ALA2K 57 " (cutoff:3.500A) Processing helix chain '2K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2K 77 " --> pdb=" O GLN2K 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU2K 78 " --> pdb=" O SER2K 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2K 83 " --> pdb=" O GLY2K 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2K 88 " --> pdb=" O GLY2K 84 " (cutoff:3.500A) Processing helix chain '2K' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL2K 97 " --> pdb=" O SER2K 93 " (cutoff:3.500A) Processing helix chain '2K' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2K 113 " --> pdb=" O GLY2K 109 " (cutoff:3.500A) Processing helix chain '2L' and resid 55 through 68 removed outlier: 3.603A pdb=" N MET2L 59 " --> pdb=" O ASP2L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2L 61 " --> pdb=" O ALA2L 57 " (cutoff:3.500A) Processing helix chain '2L' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL2L 77 " --> pdb=" O GLN2L 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2L 78 " --> pdb=" O SER2L 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2L 83 " --> pdb=" O GLY2L 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET2L 88 " --> pdb=" O GLY2L 84 " (cutoff:3.500A) Processing helix chain '2L' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2L 97 " --> pdb=" O SER2L 93 " (cutoff:3.500A) Processing helix chain '2L' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU2L 113 " --> pdb=" O GLY2L 109 " (cutoff:3.500A) Processing helix chain '2M' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET2M 59 " --> pdb=" O ASP2M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2M 61 " --> pdb=" O ALA2M 57 " (cutoff:3.500A) Processing helix chain '2M' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2M 77 " --> pdb=" O GLN2M 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2M 78 " --> pdb=" O SER2M 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2M 83 " --> pdb=" O GLY2M 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2M 88 " --> pdb=" O GLY2M 84 " (cutoff:3.500A) Processing helix chain '2M' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2M 97 " --> pdb=" O SER2M 93 " (cutoff:3.500A) Processing helix chain '2M' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2M 113 " --> pdb=" O GLY2M 109 " (cutoff:3.500A) Processing helix chain '2N' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2N 59 " --> pdb=" O ASP2N 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2N 61 " --> pdb=" O ALA2N 57 " (cutoff:3.500A) Processing helix chain '2N' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2N 77 " --> pdb=" O GLN2N 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU2N 78 " --> pdb=" O SER2N 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2N 83 " --> pdb=" O GLY2N 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2N 88 " --> pdb=" O GLY2N 84 " (cutoff:3.500A) Processing helix chain '2N' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL2N 97 " --> pdb=" O SER2N 93 " (cutoff:3.500A) Processing helix chain '2N' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2N 113 " --> pdb=" O GLY2N 109 " (cutoff:3.500A) Processing helix chain '3A' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3A 59 " --> pdb=" O ASP3A 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN3A 61 " --> pdb=" O ALA3A 57 " (cutoff:3.500A) Processing helix chain '3A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3A 77 " --> pdb=" O GLN3A 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3A 78 " --> pdb=" O SER3A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3A 83 " --> pdb=" O GLY3A 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3A 88 " --> pdb=" O GLY3A 84 " (cutoff:3.500A) Processing helix chain '3A' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3A 97 " --> pdb=" O SER3A 93 " (cutoff:3.500A) Processing helix chain '3A' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3A 113 " --> pdb=" O GLY3A 109 " (cutoff:3.500A) Processing helix chain '3B' and resid 55 through 68 removed outlier: 3.603A pdb=" N MET3B 59 " --> pdb=" O ASP3B 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3B 61 " --> pdb=" O ALA3B 57 " (cutoff:3.500A) Processing helix chain '3B' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3B 77 " --> pdb=" O GLN3B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3B 78 " --> pdb=" O SER3B 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE3B 83 " --> pdb=" O GLY3B 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3B 88 " --> pdb=" O GLY3B 84 " (cutoff:3.500A) Processing helix chain '3B' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3B 97 " --> pdb=" O SER3B 93 " (cutoff:3.500A) Processing helix chain '3B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3B 113 " --> pdb=" O GLY3B 109 " (cutoff:3.500A) Processing helix chain '3C' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3C 59 " --> pdb=" O ASP3C 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3C 61 " --> pdb=" O ALA3C 57 " (cutoff:3.500A) Processing helix chain '3C' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3C 77 " --> pdb=" O GLN3C 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3C 78 " --> pdb=" O SER3C 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE3C 83 " --> pdb=" O GLY3C 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3C 88 " --> pdb=" O GLY3C 84 " (cutoff:3.500A) Processing helix chain '3C' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3C 97 " --> pdb=" O SER3C 93 " (cutoff:3.500A) Processing helix chain '3C' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3C 113 " --> pdb=" O GLY3C 109 " (cutoff:3.500A) Processing helix chain '3D' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3D 59 " --> pdb=" O ASP3D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3D 61 " --> pdb=" O ALA3D 57 " (cutoff:3.500A) Processing helix chain '3D' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3D 77 " --> pdb=" O GLN3D 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU3D 78 " --> pdb=" O SER3D 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3D 83 " --> pdb=" O GLY3D 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3D 88 " --> pdb=" O GLY3D 84 " (cutoff:3.500A) Processing helix chain '3D' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3D 97 " --> pdb=" O SER3D 93 " (cutoff:3.500A) Processing helix chain '3D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3D 113 " --> pdb=" O GLY3D 109 " (cutoff:3.500A) Processing helix chain '3E' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3E 59 " --> pdb=" O ASP3E 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3E 61 " --> pdb=" O ALA3E 57 " (cutoff:3.500A) Processing helix chain '3E' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL3E 77 " --> pdb=" O GLN3E 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3E 78 " --> pdb=" O SER3E 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3E 83 " --> pdb=" O GLY3E 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3E 88 " --> pdb=" O GLY3E 84 " (cutoff:3.500A) Processing helix chain '3E' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3E 97 " --> pdb=" O SER3E 93 " (cutoff:3.500A) Processing helix chain '3E' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3E 113 " --> pdb=" O GLY3E 109 " (cutoff:3.500A) Processing helix chain '3F' and resid 55 through 68 removed outlier: 3.603A pdb=" N MET3F 59 " --> pdb=" O ASP3F 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN3F 61 " --> pdb=" O ALA3F 57 " (cutoff:3.500A) Processing helix chain '3F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3F 77 " --> pdb=" O GLN3F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3F 78 " --> pdb=" O SER3F 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3F 83 " --> pdb=" O GLY3F 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3F 88 " --> pdb=" O GLY3F 84 " (cutoff:3.500A) Processing helix chain '3F' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3F 97 " --> pdb=" O SER3F 93 " (cutoff:3.500A) Processing helix chain '3F' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3F 113 " --> pdb=" O GLY3F 109 " (cutoff:3.500A) Processing helix chain '3G' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3G 59 " --> pdb=" O ASP3G 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3G 61 " --> pdb=" O ALA3G 57 " (cutoff:3.500A) Processing helix chain '3G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3G 77 " --> pdb=" O GLN3G 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU3G 78 " --> pdb=" O SER3G 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3G 83 " --> pdb=" O GLY3G 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3G 88 " --> pdb=" O GLY3G 84 " (cutoff:3.500A) Processing helix chain '3G' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3G 97 " --> pdb=" O SER3G 93 " (cutoff:3.500A) Processing helix chain '3G' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU3G 113 " --> pdb=" O GLY3G 109 " (cutoff:3.500A) Processing helix chain '3H' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3H 59 " --> pdb=" O ASP3H 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN3H 61 " --> pdb=" O ALA3H 57 " (cutoff:3.500A) Processing helix chain '3H' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3H 77 " --> pdb=" O GLN3H 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3H 78 " --> pdb=" O SER3H 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3H 83 " --> pdb=" O GLY3H 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3H 88 " --> pdb=" O GLY3H 84 " (cutoff:3.500A) Processing helix chain '3H' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3H 97 " --> pdb=" O SER3H 93 " (cutoff:3.500A) Processing helix chain '3H' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3H 113 " --> pdb=" O GLY3H 109 " (cutoff:3.500A) Processing helix chain '3I' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3I 59 " --> pdb=" O ASP3I 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3I 61 " --> pdb=" O ALA3I 57 " (cutoff:3.500A) Processing helix chain '3I' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3I 77 " --> pdb=" O GLN3I 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3I 78 " --> pdb=" O SER3I 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3I 83 " --> pdb=" O GLY3I 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3I 88 " --> pdb=" O GLY3I 84 " (cutoff:3.500A) Processing helix chain '3I' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3I 97 " --> pdb=" O SER3I 93 " (cutoff:3.500A) Processing helix chain '3I' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3I 113 " --> pdb=" O GLY3I 109 " (cutoff:3.500A) Processing helix chain '3J' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3J 59 " --> pdb=" O ASP3J 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3J 61 " --> pdb=" O ALA3J 57 " (cutoff:3.500A) Processing helix chain '3J' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3J 77 " --> pdb=" O GLN3J 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3J 78 " --> pdb=" O SER3J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3J 83 " --> pdb=" O GLY3J 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3J 88 " --> pdb=" O GLY3J 84 " (cutoff:3.500A) Processing helix chain '3J' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3J 97 " --> pdb=" O SER3J 93 " (cutoff:3.500A) Processing helix chain '3J' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3J 113 " --> pdb=" O GLY3J 109 " (cutoff:3.500A) Processing helix chain '3K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3K 59 " --> pdb=" O ASP3K 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3K 61 " --> pdb=" O ALA3K 57 " (cutoff:3.500A) Processing helix chain '3K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3K 77 " --> pdb=" O GLN3K 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3K 78 " --> pdb=" O SER3K 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE3K 83 " --> pdb=" O GLY3K 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3K 88 " --> pdb=" O GLY3K 84 " (cutoff:3.500A) Processing helix chain '3K' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3K 97 " --> pdb=" O SER3K 93 " (cutoff:3.500A) Processing helix chain '3K' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3K 113 " --> pdb=" O GLY3K 109 " (cutoff:3.500A) Processing helix chain '3L' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3L 59 " --> pdb=" O ASP3L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3L 61 " --> pdb=" O ALA3L 57 " (cutoff:3.500A) Processing helix chain '3L' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL3L 77 " --> pdb=" O GLN3L 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3L 78 " --> pdb=" O SER3L 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3L 83 " --> pdb=" O GLY3L 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3L 88 " --> pdb=" O GLY3L 84 " (cutoff:3.500A) Processing helix chain '3L' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3L 97 " --> pdb=" O SER3L 93 " (cutoff:3.500A) Processing helix chain '3L' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3L 113 " --> pdb=" O GLY3L 109 " (cutoff:3.500A) Processing helix chain '3M' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3M 59 " --> pdb=" O ASP3M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3M 61 " --> pdb=" O ALA3M 57 " (cutoff:3.500A) Processing helix chain '3M' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3M 77 " --> pdb=" O GLN3M 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3M 78 " --> pdb=" O SER3M 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3M 83 " --> pdb=" O GLY3M 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3M 88 " --> pdb=" O GLY3M 84 " (cutoff:3.500A) Processing helix chain '3M' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3M 97 " --> pdb=" O SER3M 93 " (cutoff:3.500A) Processing helix chain '3M' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3M 113 " --> pdb=" O GLY3M 109 " (cutoff:3.500A) Processing helix chain '3N' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3N 59 " --> pdb=" O ASP3N 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3N 61 " --> pdb=" O ALA3N 57 " (cutoff:3.500A) Processing helix chain '3N' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3N 77 " --> pdb=" O GLN3N 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3N 78 " --> pdb=" O SER3N 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE3N 83 " --> pdb=" O GLY3N 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3N 88 " --> pdb=" O GLY3N 84 " (cutoff:3.500A) Processing helix chain '3N' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3N 97 " --> pdb=" O SER3N 93 " (cutoff:3.500A) Processing helix chain '3N' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3N 113 " --> pdb=" O GLY3N 109 " (cutoff:3.500A) Processing helix chain '4A' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4A 59 " --> pdb=" O ASP4A 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN4A 61 " --> pdb=" O ALA4A 57 " (cutoff:3.500A) Processing helix chain '4A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4A 77 " --> pdb=" O GLN4A 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4A 78 " --> pdb=" O SER4A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4A 83 " --> pdb=" O GLY4A 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4A 88 " --> pdb=" O GLY4A 84 " (cutoff:3.500A) Processing helix chain '4A' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4A 97 " --> pdb=" O SER4A 93 " (cutoff:3.500A) Processing helix chain '4A' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4A 113 " --> pdb=" O GLY4A 109 " (cutoff:3.500A) Processing helix chain '4B' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET4B 59 " --> pdb=" O ASP4B 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4B 61 " --> pdb=" O ALA4B 57 " (cutoff:3.500A) Processing helix chain '4B' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4B 77 " --> pdb=" O GLN4B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4B 78 " --> pdb=" O SER4B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4B 83 " --> pdb=" O GLY4B 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4B 88 " --> pdb=" O GLY4B 84 " (cutoff:3.500A) Processing helix chain '4B' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4B 97 " --> pdb=" O SER4B 93 " (cutoff:3.500A) Processing helix chain '4B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4B 113 " --> pdb=" O GLY4B 109 " (cutoff:3.500A) Processing helix chain '4C' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4C 59 " --> pdb=" O ASP4C 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4C 61 " --> pdb=" O ALA4C 57 " (cutoff:3.500A) Processing helix chain '4C' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL4C 77 " --> pdb=" O GLN4C 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4C 78 " --> pdb=" O SER4C 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE4C 83 " --> pdb=" O GLY4C 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4C 88 " --> pdb=" O GLY4C 84 " (cutoff:3.500A) Processing helix chain '4C' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4C 97 " --> pdb=" O SER4C 93 " (cutoff:3.500A) Processing helix chain '4C' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4C 113 " --> pdb=" O GLY4C 109 " (cutoff:3.500A) Processing helix chain '4D' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4D 59 " --> pdb=" O ASP4D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4D 61 " --> pdb=" O ALA4D 57 " (cutoff:3.500A) Processing helix chain '4D' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4D 77 " --> pdb=" O GLN4D 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4D 78 " --> pdb=" O SER4D 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4D 83 " --> pdb=" O GLY4D 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4D 88 " --> pdb=" O GLY4D 84 " (cutoff:3.500A) Processing helix chain '4D' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4D 97 " --> pdb=" O SER4D 93 " (cutoff:3.500A) Processing helix chain '4D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4D 113 " --> pdb=" O GLY4D 109 " (cutoff:3.500A) Processing helix chain '4E' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4E 59 " --> pdb=" O ASP4E 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4E 61 " --> pdb=" O ALA4E 57 " (cutoff:3.500A) Processing helix chain '4E' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4E 77 " --> pdb=" O GLN4E 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU4E 78 " --> pdb=" O SER4E 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4E 83 " --> pdb=" O GLY4E 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4E 88 " --> pdb=" O GLY4E 84 " (cutoff:3.500A) Processing helix chain '4E' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL4E 97 " --> pdb=" O SER4E 93 " (cutoff:3.500A) Processing helix chain '4E' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4E 113 " --> pdb=" O GLY4E 109 " (cutoff:3.500A) Processing helix chain '4F' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4F 59 " --> pdb=" O ASP4F 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4F 61 " --> pdb=" O ALA4F 57 " (cutoff:3.500A) Processing helix chain '4F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4F 77 " --> pdb=" O GLN4F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4F 78 " --> pdb=" O SER4F 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4F 83 " --> pdb=" O GLY4F 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4F 88 " --> pdb=" O GLY4F 84 " (cutoff:3.500A) Processing helix chain '4F' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4F 97 " --> pdb=" O SER4F 93 " (cutoff:3.500A) Processing helix chain '4F' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU4F 113 " --> pdb=" O GLY4F 109 " (cutoff:3.500A) Processing helix chain '4G' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET4G 59 " --> pdb=" O ASP4G 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4G 61 " --> pdb=" O ALA4G 57 " (cutoff:3.500A) Processing helix chain '4G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4G 77 " --> pdb=" O GLN4G 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4G 78 " --> pdb=" O SER4G 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE4G 83 " --> pdb=" O GLY4G 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4G 88 " --> pdb=" O GLY4G 84 " (cutoff:3.500A) Processing helix chain '4G' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL4G 97 " --> pdb=" O SER4G 93 " (cutoff:3.500A) Processing helix chain '4G' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4G 113 " --> pdb=" O GLY4G 109 " (cutoff:3.500A) Processing helix chain '4H' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4H 59 " --> pdb=" O ASP4H 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4H 61 " --> pdb=" O ALA4H 57 " (cutoff:3.500A) Processing helix chain '4H' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL4H 77 " --> pdb=" O GLN4H 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4H 78 " --> pdb=" O SER4H 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4H 83 " --> pdb=" O GLY4H 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4H 88 " --> pdb=" O GLY4H 84 " (cutoff:3.500A) Processing helix chain '4H' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4H 97 " --> pdb=" O SER4H 93 " (cutoff:3.500A) Processing helix chain '4H' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU4H 113 " --> pdb=" O GLY4H 109 " (cutoff:3.500A) Processing helix chain '4I' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET4I 59 " --> pdb=" O ASP4I 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4I 61 " --> pdb=" O ALA4I 57 " (cutoff:3.500A) Processing helix chain '4I' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4I 77 " --> pdb=" O GLN4I 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4I 78 " --> pdb=" O SER4I 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4I 83 " --> pdb=" O GLY4I 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4I 88 " --> pdb=" O GLY4I 84 " (cutoff:3.500A) Processing helix chain '4I' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4I 97 " --> pdb=" O SER4I 93 " (cutoff:3.500A) Processing helix chain '4I' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4I 113 " --> pdb=" O GLY4I 109 " (cutoff:3.500A) Processing helix chain '4J' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4J 59 " --> pdb=" O ASP4J 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4J 61 " --> pdb=" O ALA4J 57 " (cutoff:3.500A) Processing helix chain '4J' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL4J 77 " --> pdb=" O GLN4J 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4J 78 " --> pdb=" O SER4J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4J 83 " --> pdb=" O GLY4J 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4J 88 " --> pdb=" O GLY4J 84 " (cutoff:3.500A) Processing helix chain '4J' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4J 97 " --> pdb=" O SER4J 93 " (cutoff:3.500A) Processing helix chain '4J' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4J 113 " --> pdb=" O GLY4J 109 " (cutoff:3.500A) Processing helix chain '4K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4K 59 " --> pdb=" O ASP4K 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4K 61 " --> pdb=" O ALA4K 57 " (cutoff:3.500A) Processing helix chain '4K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4K 77 " --> pdb=" O GLN4K 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4K 78 " --> pdb=" O SER4K 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4K 83 " --> pdb=" O GLY4K 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4K 88 " --> pdb=" O GLY4K 84 " (cutoff:3.500A) Processing helix chain '4K' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4K 97 " --> pdb=" O SER4K 93 " (cutoff:3.500A) Processing helix chain '4K' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4K 113 " --> pdb=" O GLY4K 109 " (cutoff:3.500A) Processing helix chain '4L' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4L 59 " --> pdb=" O ASP4L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4L 61 " --> pdb=" O ALA4L 57 " (cutoff:3.500A) Processing helix chain '4L' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4L 77 " --> pdb=" O GLN4L 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4L 78 " --> pdb=" O SER4L 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE4L 83 " --> pdb=" O GLY4L 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4L 88 " --> pdb=" O GLY4L 84 " (cutoff:3.500A) Processing helix chain '4L' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4L 97 " --> pdb=" O SER4L 93 " (cutoff:3.500A) Processing helix chain '4L' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4L 113 " --> pdb=" O GLY4L 109 " (cutoff:3.500A) Processing helix chain '4M' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4M 59 " --> pdb=" O ASP4M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4M 61 " --> pdb=" O ALA4M 57 " (cutoff:3.500A) Processing helix chain '4M' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4M 77 " --> pdb=" O GLN4M 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4M 78 " --> pdb=" O SER4M 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4M 83 " --> pdb=" O GLY4M 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4M 88 " --> pdb=" O GLY4M 84 " (cutoff:3.500A) Processing helix chain '4M' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL4M 97 " --> pdb=" O SER4M 93 " (cutoff:3.500A) Processing helix chain '4M' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4M 113 " --> pdb=" O GLY4M 109 " (cutoff:3.500A) Processing helix chain '4N' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4N 59 " --> pdb=" O ASP4N 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4N 61 " --> pdb=" O ALA4N 57 " (cutoff:3.500A) Processing helix chain '4N' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4N 77 " --> pdb=" O GLN4N 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4N 78 " --> pdb=" O SER4N 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4N 83 " --> pdb=" O GLY4N 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4N 88 " --> pdb=" O GLY4N 84 " (cutoff:3.500A) Processing helix chain '4N' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4N 97 " --> pdb=" O SER4N 93 " (cutoff:3.500A) Processing helix chain '4N' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4N 113 " --> pdb=" O GLY4N 109 " (cutoff:3.500A) Processing helix chain '5A' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET5A 59 " --> pdb=" O ASP5A 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN5A 61 " --> pdb=" O ALA5A 57 " (cutoff:3.500A) Processing helix chain '5A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5A 77 " --> pdb=" O GLN5A 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5A 78 " --> pdb=" O SER5A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5A 83 " --> pdb=" O GLY5A 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5A 88 " --> pdb=" O GLY5A 84 " (cutoff:3.500A) Processing helix chain '5A' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5A 97 " --> pdb=" O SER5A 93 " (cutoff:3.500A) Processing helix chain '5A' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5A 113 " --> pdb=" O GLY5A 109 " (cutoff:3.500A) Processing helix chain '5B' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET5B 59 " --> pdb=" O ASP5B 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN5B 61 " --> pdb=" O ALA5B 57 " (cutoff:3.500A) Processing helix chain '5B' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5B 77 " --> pdb=" O GLN5B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5B 78 " --> pdb=" O SER5B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5B 83 " --> pdb=" O GLY5B 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5B 88 " --> pdb=" O GLY5B 84 " (cutoff:3.500A) Processing helix chain '5B' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5B 97 " --> pdb=" O SER5B 93 " (cutoff:3.500A) Processing helix chain '5B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5B 113 " --> pdb=" O GLY5B 109 " (cutoff:3.500A) Processing helix chain '5C' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5C 59 " --> pdb=" O ASP5C 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN5C 61 " --> pdb=" O ALA5C 57 " (cutoff:3.500A) Processing helix chain '5C' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL5C 77 " --> pdb=" O GLN5C 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5C 78 " --> pdb=" O SER5C 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5C 83 " --> pdb=" O GLY5C 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET5C 88 " --> pdb=" O GLY5C 84 " (cutoff:3.500A) Processing helix chain '5C' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5C 97 " --> pdb=" O SER5C 93 " (cutoff:3.500A) Processing helix chain '5C' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5C 113 " --> pdb=" O GLY5C 109 " (cutoff:3.500A) Processing helix chain '5D' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET5D 59 " --> pdb=" O ASP5D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5D 61 " --> pdb=" O ALA5D 57 " (cutoff:3.500A) Processing helix chain '5D' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5D 77 " --> pdb=" O GLN5D 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5D 78 " --> pdb=" O SER5D 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE5D 83 " --> pdb=" O GLY5D 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5D 88 " --> pdb=" O GLY5D 84 " (cutoff:3.500A) Processing helix chain '5D' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5D 97 " --> pdb=" O SER5D 93 " (cutoff:3.500A) Processing helix chain '5D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5D 113 " --> pdb=" O GLY5D 109 " (cutoff:3.500A) Processing helix chain '5E' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5E 59 " --> pdb=" O ASP5E 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN5E 61 " --> pdb=" O ALA5E 57 " (cutoff:3.500A) Processing helix chain '5E' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5E 77 " --> pdb=" O GLN5E 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5E 78 " --> pdb=" O SER5E 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE5E 83 " --> pdb=" O GLY5E 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET5E 88 " --> pdb=" O GLY5E 84 " (cutoff:3.500A) Processing helix chain '5E' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5E 97 " --> pdb=" O SER5E 93 " (cutoff:3.500A) Processing helix chain '5E' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5E 113 " --> pdb=" O GLY5E 109 " (cutoff:3.500A) Processing helix chain '5F' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5F 59 " --> pdb=" O ASP5F 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5F 61 " --> pdb=" O ALA5F 57 " (cutoff:3.500A) Processing helix chain '5F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5F 77 " --> pdb=" O GLN5F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5F 78 " --> pdb=" O SER5F 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5F 83 " --> pdb=" O GLY5F 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5F 88 " --> pdb=" O GLY5F 84 " (cutoff:3.500A) Processing helix chain '5F' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5F 97 " --> pdb=" O SER5F 93 " (cutoff:3.500A) Processing helix chain '5F' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5F 113 " --> pdb=" O GLY5F 109 " (cutoff:3.500A) Processing helix chain '5G' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5G 59 " --> pdb=" O ASP5G 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN5G 61 " --> pdb=" O ALA5G 57 " (cutoff:3.500A) Processing helix chain '5G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5G 77 " --> pdb=" O GLN5G 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5G 78 " --> pdb=" O SER5G 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5G 83 " --> pdb=" O GLY5G 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5G 88 " --> pdb=" O GLY5G 84 " (cutoff:3.500A) Processing helix chain '5G' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5G 97 " --> pdb=" O SER5G 93 " (cutoff:3.500A) Processing helix chain '5G' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5G 113 " --> pdb=" O GLY5G 109 " (cutoff:3.500A) Processing helix chain '5H' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5H 59 " --> pdb=" O ASP5H 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5H 61 " --> pdb=" O ALA5H 57 " (cutoff:3.500A) Processing helix chain '5H' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5H 77 " --> pdb=" O GLN5H 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU5H 78 " --> pdb=" O SER5H 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE5H 83 " --> pdb=" O GLY5H 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5H 88 " --> pdb=" O GLY5H 84 " (cutoff:3.500A) Processing helix chain '5H' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5H 97 " --> pdb=" O SER5H 93 " (cutoff:3.500A) Processing helix chain '5H' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5H 113 " --> pdb=" O GLY5H 109 " (cutoff:3.500A) Processing helix chain '5I' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5I 59 " --> pdb=" O ASP5I 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN5I 61 " --> pdb=" O ALA5I 57 " (cutoff:3.500A) Processing helix chain '5I' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5I 77 " --> pdb=" O GLN5I 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5I 78 " --> pdb=" O SER5I 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5I 83 " --> pdb=" O GLY5I 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5I 88 " --> pdb=" O GLY5I 84 " (cutoff:3.500A) Processing helix chain '5I' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5I 97 " --> pdb=" O SER5I 93 " (cutoff:3.500A) Processing helix chain '5I' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5I 113 " --> pdb=" O GLY5I 109 " (cutoff:3.500A) Processing helix chain '5J' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET5J 59 " --> pdb=" O ASP5J 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5J 61 " --> pdb=" O ALA5J 57 " (cutoff:3.500A) Processing helix chain '5J' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5J 77 " --> pdb=" O GLN5J 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5J 78 " --> pdb=" O SER5J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5J 83 " --> pdb=" O GLY5J 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET5J 88 " --> pdb=" O GLY5J 84 " (cutoff:3.500A) Processing helix chain '5J' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5J 97 " --> pdb=" O SER5J 93 " (cutoff:3.500A) Processing helix chain '5J' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5J 113 " --> pdb=" O GLY5J 109 " (cutoff:3.500A) Processing helix chain '5K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5K 59 " --> pdb=" O ASP5K 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5K 61 " --> pdb=" O ALA5K 57 " (cutoff:3.500A) Processing helix chain '5K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5K 77 " --> pdb=" O GLN5K 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU5K 78 " --> pdb=" O SER5K 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5K 83 " --> pdb=" O GLY5K 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET5K 88 " --> pdb=" O GLY5K 84 " (cutoff:3.500A) Processing helix chain '5K' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5K 97 " --> pdb=" O SER5K 93 " (cutoff:3.500A) Processing helix chain '5K' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5K 113 " --> pdb=" O GLY5K 109 " (cutoff:3.500A) Processing helix chain '5L' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5L 59 " --> pdb=" O ASP5L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5L 61 " --> pdb=" O ALA5L 57 " (cutoff:3.500A) Processing helix chain '5L' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5L 77 " --> pdb=" O GLN5L 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU5L 78 " --> pdb=" O SER5L 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE5L 83 " --> pdb=" O GLY5L 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5L 88 " --> pdb=" O GLY5L 84 " (cutoff:3.500A) Processing helix chain '5L' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5L 97 " --> pdb=" O SER5L 93 " (cutoff:3.500A) Processing helix chain '5L' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5L 113 " --> pdb=" O GLY5L 109 " (cutoff:3.500A) Processing helix chain '5M' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5M 59 " --> pdb=" O ASP5M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5M 61 " --> pdb=" O ALA5M 57 " (cutoff:3.500A) Processing helix chain '5M' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL5M 77 " --> pdb=" O GLN5M 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU5M 78 " --> pdb=" O SER5M 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE5M 83 " --> pdb=" O GLY5M 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET5M 88 " --> pdb=" O GLY5M 84 " (cutoff:3.500A) Processing helix chain '5M' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5M 97 " --> pdb=" O SER5M 93 " (cutoff:3.500A) Processing helix chain '5M' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5M 113 " --> pdb=" O GLY5M 109 " (cutoff:3.500A) Processing helix chain '5N' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5N 59 " --> pdb=" O ASP5N 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN5N 61 " --> pdb=" O ALA5N 57 " (cutoff:3.500A) Processing helix chain '5N' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL5N 77 " --> pdb=" O GLN5N 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5N 78 " --> pdb=" O SER5N 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5N 83 " --> pdb=" O GLY5N 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5N 88 " --> pdb=" O GLY5N 84 " (cutoff:3.500A) Processing helix chain '5N' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5N 97 " --> pdb=" O SER5N 93 " (cutoff:3.500A) Processing helix chain '5N' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5N 113 " --> pdb=" O GLY5N 109 " (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: 5.85 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5390 1.31 - 1.43: 9234 1.43 - 1.56: 22409 1.56 - 1.68: 207 1.68 - 1.81: 490 Bond restraints: 37730 Sorted by residual: bond pdb=" C11 CPL3A 201 " pdb=" O3 CPL3A 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C11 CPL5F 201 " pdb=" O3 CPL5F 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C11 CPL1M 201 " pdb=" O3 CPL1M 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C11 CPL5G 201 " pdb=" O3 CPL5G 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C11 CPL1A 201 " pdb=" O3 CPL1A 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 37725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.25: 49490 5.25 - 10.50: 630 10.50 - 15.75: 0 15.75 - 21.00: 70 21.00 - 26.25: 140 Bond angle restraints: 50330 Sorted by residual: angle pdb=" C39 CPL5B 201 " pdb=" C40 CPL5B 201 " pdb=" C41 CPL5B 201 " ideal model delta sigma weight residual 127.51 153.76 -26.25 3.00e+00 1.11e-01 7.66e+01 angle pdb=" C39 CPL3B 201 " pdb=" C40 CPL3B 201 " pdb=" C41 CPL3B 201 " ideal model delta sigma weight residual 127.51 153.75 -26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C39 CPL1L 201 " pdb=" C40 CPL1L 201 " pdb=" C41 CPL1L 201 " ideal model delta sigma weight residual 127.51 153.75 -26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C39 CPL5D 201 " pdb=" C40 CPL5D 201 " pdb=" C41 CPL5D 201 " ideal model delta sigma weight residual 127.51 153.75 -26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C39 CPL5F 201 " pdb=" C40 CPL5F 201 " pdb=" C41 CPL5F 201 " ideal model delta sigma weight residual 127.51 153.74 -26.23 3.00e+00 1.11e-01 7.65e+01 ... (remaining 50325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 20300 35.84 - 71.67: 1120 71.67 - 107.51: 210 107.51 - 143.35: 0 143.35 - 179.18: 70 Dihedral angle restraints: 21700 sinusoidal: 9310 harmonic: 12390 Sorted by residual: dihedral pdb=" C33 CPL1D 201 " pdb=" C31 CPL1D 201 " pdb=" C32 CPL1D 201 " pdb=" O2 CPL1D 201 " ideal model delta sinusoidal sigma weight residual 171.65 -9.17 -179.18 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 CPL3M 201 " pdb=" C31 CPL3M 201 " pdb=" C32 CPL3M 201 " pdb=" O2 CPL3M 201 " ideal model delta sinusoidal sigma weight residual 171.65 -9.18 -179.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 CPL3F 201 " pdb=" C31 CPL3F 201 " pdb=" C32 CPL3F 201 " pdb=" O2 CPL3F 201 " ideal model delta sinusoidal sigma weight residual 171.65 -9.18 -179.17 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 21697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4627 0.047 - 0.093: 904 0.093 - 0.140: 69 0.140 - 0.187: 0 0.187 - 0.233: 70 Chirality restraints: 5670 Sorted by residual: chirality pdb=" C2 CPL2H 201 " pdb=" C1 CPL2H 201 " pdb=" C3 CPL2H 201 " pdb=" O2 CPL2H 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C2 CPL4L 201 " pdb=" C1 CPL4L 201 " pdb=" C3 CPL4L 201 " pdb=" O2 CPL4L 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C2 CPL5L 201 " pdb=" C1 CPL5L 201 " pdb=" C3 CPL5L 201 " pdb=" O2 CPL5L 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 5667 not shown) Planarity restraints: 6020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP1A 55 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.59e-01 pdb=" N PRO1A 56 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO1A 56 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO1A 56 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP1L 55 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.56e-01 pdb=" N PRO1L 56 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO1L 56 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO1L 56 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP5C 55 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.55e-01 pdb=" N PRO5C 56 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO5C 56 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO5C 56 " -0.012 5.00e-02 4.00e+02 ... (remaining 6017 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 20275 3.01 - 3.48: 34926 3.48 - 3.96: 57404 3.96 - 4.43: 64413 4.43 - 4.90: 108145 Nonbonded interactions: 285163 Sorted by model distance: nonbonded pdb=" OD1 ASP1H 55 " pdb=" OG1 THR1H 58 " model vdw 2.541 3.040 nonbonded pdb=" OD1 ASP1K 55 " pdb=" OG1 THR1K 58 " model vdw 2.541 3.040 nonbonded pdb=" OD1 ASP2L 55 " pdb=" OG1 THR2L 58 " model vdw 2.541 3.040 nonbonded pdb=" OD1 ASP2C 55 " pdb=" OG1 THR2C 58 " model vdw 2.541 3.040 nonbonded pdb=" OD1 ASP2K 55 " pdb=" OG1 THR2K 58 " model vdw 2.542 3.040 ... (remaining 285158 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: 0.13 Found NCS groups: ncs_group { reference = chain '1A' selection = chain '1B' selection = chain '1C' selection = chain '1D' selection = chain '1E' selection = chain '1F' selection = chain '1G' selection = chain '1H' selection = chain '1I' selection = chain '1J' selection = chain '1K' selection = chain '1L' selection = chain '1M' selection = chain '1N' selection = chain '2A' selection = chain '2B' selection = chain '2C' selection = chain '2D' selection = chain '2E' selection = chain '2F' selection = chain '2G' selection = chain '2H' selection = chain '2I' selection = chain '2J' selection = chain '2K' selection = chain '2L' selection = chain '2M' selection = chain '2N' selection = chain '3A' selection = chain '3B' selection = chain '3C' selection = chain '3D' selection = chain '3E' selection = chain '3F' selection = chain '3G' selection = chain '3H' selection = chain '3I' selection = chain '3J' selection = chain '3K' selection = chain '3L' selection = chain '3M' selection = chain '3N' selection = chain '4A' selection = chain '4B' selection = chain '4C' selection = chain '4D' selection = chain '4E' selection = chain '4F' selection = chain '4G' selection = chain '4H' selection = chain '4I' selection = chain '4J' selection = chain '4K' selection = chain '4L' selection = chain '4M' selection = chain '4N' selection = chain '5A' selection = chain '5B' selection = chain '5C' selection = chain '5D' selection = chain '5E' selection = chain '5F' selection = chain '5G' selection = chain '5H' selection = chain '5I' selection = chain '5J' selection = chain '5K' selection = chain '5L' selection = chain '5M' selection = chain '5N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.300 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.010 0.097 37730 Z= 0.524 Angle : 1.825 26.252 50330 Z= 0.629 Chirality : 0.042 0.233 5670 Planarity : 0.003 0.022 6020 Dihedral : 24.543 179.182 14140 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.11), residues: 4760 helix: 0.64 (0.07), residues: 3920 sheet: None (None), residues: 0 loop : 0.53 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG4I 91 PHE 0.005 0.001 PHE2F 89 TRP 0.012 0.002 TRP3H 87 Details of bonding type rmsd covalent geometry : bond 0.01049 (37730) covalent geometry : angle 1.82490 (50330) hydrogen bonds : bond 0.24306 ( 2590) hydrogen bonds : angle 6.37538 ( 7770) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 810 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8766 (mtt) cc_final: 0.8449 (mtt) REVERT: 1B 59 MET cc_start: 0.8858 (mtt) cc_final: 0.8550 (mtt) REVERT: 1E 107 MET cc_start: 0.8806 (ttt) cc_final: 0.8554 (ttt) REVERT: 1F 107 MET cc_start: 0.8765 (ttt) cc_final: 0.8392 (ttt) REVERT: 1G 115 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7991 (ttmm) REVERT: 1I 107 MET cc_start: 0.8884 (ttt) cc_final: 0.8603 (ttp) REVERT: 1J 107 MET cc_start: 0.8696 (ttt) cc_final: 0.8356 (ttp) REVERT: 1J 117 LEU cc_start: 0.8749 (tp) cc_final: 0.8538 (tt) REVERT: 1K 59 MET cc_start: 0.8783 (mtt) cc_final: 0.8531 (mtt) REVERT: 1K 107 MET cc_start: 0.8784 (ttt) cc_final: 0.8437 (ttp) REVERT: 1L 107 MET cc_start: 0.8680 (ttt) cc_final: 0.8456 (ttt) REVERT: 1M 107 MET cc_start: 0.8610 (ttt) cc_final: 0.8345 (ttt) REVERT: 2A 59 MET cc_start: 0.8793 (mtt) cc_final: 0.8342 (mtt) REVERT: 2B 59 MET cc_start: 0.8767 (mtt) cc_final: 0.8265 (mtt) REVERT: 2E 59 MET cc_start: 0.8657 (mtt) cc_final: 0.8389 (mtt) REVERT: 2E 107 MET cc_start: 0.8737 (ttt) cc_final: 0.8469 (ttt) REVERT: 2H 107 MET cc_start: 0.8866 (ttt) cc_final: 0.8590 (ttt) REVERT: 2J 59 MET cc_start: 0.8773 (mtt) cc_final: 0.8484 (mtt) REVERT: 2J 107 MET cc_start: 0.8646 (ttt) cc_final: 0.8434 (ttp) REVERT: 2J 117 LEU cc_start: 0.8832 (tp) cc_final: 0.8610 (tt) REVERT: 2K 59 MET cc_start: 0.8720 (mtt) cc_final: 0.8513 (mtt) REVERT: 2L 107 MET cc_start: 0.8569 (ttt) cc_final: 0.8324 (ttp) REVERT: 2M 107 MET cc_start: 0.8438 (ttt) cc_final: 0.8141 (ttt) REVERT: 3B 59 MET cc_start: 0.8680 (mtt) cc_final: 0.8397 (mtt) REVERT: 3E 107 MET cc_start: 0.8765 (ttt) cc_final: 0.8387 (ttp) REVERT: 3G 59 MET cc_start: 0.8576 (mtt) cc_final: 0.8132 (mtt) REVERT: 3G 107 MET cc_start: 0.8885 (ttt) cc_final: 0.8623 (ttt) REVERT: 3K 107 MET cc_start: 0.8803 (ttt) cc_final: 0.8516 (ttt) REVERT: 3K 112 PHE cc_start: 0.8262 (m-80) cc_final: 0.7902 (m-80) REVERT: 3L 59 MET cc_start: 0.8710 (mtt) cc_final: 0.8425 (mtt) REVERT: 3L 107 MET cc_start: 0.8703 (ttt) cc_final: 0.8414 (ttp) REVERT: 3M 107 MET cc_start: 0.8525 (ttt) cc_final: 0.8287 (ttp) REVERT: 4B 107 MET cc_start: 0.8804 (ttt) cc_final: 0.8580 (ttt) REVERT: 4G 59 MET cc_start: 0.8674 (mtt) cc_final: 0.8419 (mtt) REVERT: 4H 59 MET cc_start: 0.8671 (mtt) cc_final: 0.8345 (mtt) REVERT: 4I 59 MET cc_start: 0.8625 (mtt) cc_final: 0.8328 (mtt) REVERT: 4I 107 MET cc_start: 0.8803 (ttt) cc_final: 0.8599 (ttp) REVERT: 4I 115 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7812 (mptt) REVERT: 4K 59 MET cc_start: 0.8857 (mtt) cc_final: 0.8613 (mtt) REVERT: 4K 112 PHE cc_start: 0.8062 (m-80) cc_final: 0.7828 (m-80) REVERT: 4N 61 ASN cc_start: 0.8241 (m-40) cc_final: 0.7985 (m-40) REVERT: 5G 59 MET cc_start: 0.8606 (mtt) cc_final: 0.8382 (mtt) REVERT: 5I 107 MET cc_start: 0.8760 (ttt) cc_final: 0.8510 (ttp) REVERT: 5K 59 MET cc_start: 0.8831 (mtt) cc_final: 0.8429 (mtt) REVERT: 5N 61 ASN cc_start: 0.8292 (m-40) cc_final: 0.8065 (m-40) outliers start: 0 outliers final: 0 residues processed: 810 average time/residue: 0.2369 time to fit residues: 306.0973 Evaluate side-chains 652 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 432 optimal weight: 0.3980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.0070 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 5.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.093765 restraints weight = 44020.243| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.81 r_work: 0.2999 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 37730 Z= 0.111 Angle : 0.458 7.905 50330 Z= 0.238 Chirality : 0.034 0.106 5670 Planarity : 0.003 0.024 6020 Dihedral : 25.360 179.696 7910 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.57 % Allowed : 7.44 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.12), residues: 4760 helix: 2.13 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -0.91 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG5G 91 PHE 0.009 0.001 PHE3M 89 TRP 0.015 0.002 TRP4L 87 Details of bonding type rmsd covalent geometry : bond 0.00232 (37730) covalent geometry : angle 0.45769 (50330) hydrogen bonds : bond 0.04084 ( 2590) hydrogen bonds : angle 3.88788 ( 7770) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 688 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8000 (mtt) cc_final: 0.7649 (mtt) REVERT: 1A 73 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7570 (mm-40) REVERT: 1B 59 MET cc_start: 0.8383 (mtt) cc_final: 0.8045 (mtt) REVERT: 1C 107 MET cc_start: 0.8817 (ttt) cc_final: 0.8593 (ttp) REVERT: 1E 107 MET cc_start: 0.8875 (ttt) cc_final: 0.8607 (ttt) REVERT: 1F 107 MET cc_start: 0.8745 (ttt) cc_final: 0.8433 (ttp) REVERT: 1J 107 MET cc_start: 0.8729 (ttt) cc_final: 0.8527 (ttp) REVERT: 1K 112 PHE cc_start: 0.8092 (m-80) cc_final: 0.7740 (m-80) REVERT: 1L 107 MET cc_start: 0.8774 (ttt) cc_final: 0.8465 (ttt) REVERT: 1M 73 GLN cc_start: 0.8410 (mm110) cc_final: 0.8189 (mm-40) REVERT: 1M 107 MET cc_start: 0.8449 (ttt) cc_final: 0.8109 (ttt) REVERT: 2A 59 MET cc_start: 0.8295 (mtt) cc_final: 0.7810 (mtt) REVERT: 2A 68 LEU cc_start: 0.7975 (mt) cc_final: 0.7727 (mt) REVERT: 2A 73 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7640 (mm-40) REVERT: 2B 59 MET cc_start: 0.8261 (mtt) cc_final: 0.7831 (mtt) REVERT: 2E 59 MET cc_start: 0.8334 (mtt) cc_final: 0.7863 (mtt) REVERT: 2H 107 MET cc_start: 0.8998 (ttt) cc_final: 0.8720 (ttt) REVERT: 2J 59 MET cc_start: 0.8428 (mtt) cc_final: 0.8162 (mtt) REVERT: 2K 59 MET cc_start: 0.8385 (mtt) cc_final: 0.8130 (mtt) REVERT: 2L 73 GLN cc_start: 0.8696 (mt0) cc_final: 0.8337 (mm110) REVERT: 2N 58 THR cc_start: 0.7880 (m) cc_final: 0.7659 (p) REVERT: 3C 73 GLN cc_start: 0.8309 (mt0) cc_final: 0.8051 (mm-40) REVERT: 3E 107 MET cc_start: 0.8892 (ttt) cc_final: 0.8499 (ttp) REVERT: 3E 112 PHE cc_start: 0.8073 (m-80) cc_final: 0.7793 (m-80) REVERT: 3G 107 MET cc_start: 0.8839 (ttt) cc_final: 0.8551 (ttp) REVERT: 3J 107 MET cc_start: 0.8826 (ttt) cc_final: 0.8564 (ttp) REVERT: 3K 107 MET cc_start: 0.8868 (ttt) cc_final: 0.8616 (ttp) REVERT: 3K 112 PHE cc_start: 0.8252 (m-80) cc_final: 0.7971 (m-80) REVERT: 3L 107 MET cc_start: 0.8661 (ttt) cc_final: 0.8276 (ttp) REVERT: 3M 107 MET cc_start: 0.8659 (ttt) cc_final: 0.8388 (ttp) REVERT: 3N 61 ASN cc_start: 0.8349 (m-40) cc_final: 0.8133 (m-40) REVERT: 4A 73 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7671 (mm-40) REVERT: 4B 107 MET cc_start: 0.8467 (ttt) cc_final: 0.8224 (ttp) REVERT: 4B 115 LYS cc_start: 0.7586 (mtpp) cc_final: 0.7271 (ttpp) REVERT: 4G 59 MET cc_start: 0.8455 (mtt) cc_final: 0.8165 (mtt) REVERT: 4H 59 MET cc_start: 0.8429 (mtt) cc_final: 0.8145 (mtt) REVERT: 4I 59 MET cc_start: 0.8350 (mtt) cc_final: 0.8007 (mtt) REVERT: 4K 59 MET cc_start: 0.8481 (mtt) cc_final: 0.8229 (mtt) REVERT: 4L 73 GLN cc_start: 0.8545 (mt0) cc_final: 0.8145 (mm110) REVERT: 4M 61 ASN cc_start: 0.8348 (m-40) cc_final: 0.8062 (m110) REVERT: 4M 115 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7630 (ttmm) REVERT: 4N 61 ASN cc_start: 0.8315 (m-40) cc_final: 0.7947 (m-40) REVERT: 5A 108 PHE cc_start: 0.6765 (m-80) cc_final: 0.6383 (m-80) REVERT: 5E 107 MET cc_start: 0.8872 (ttt) cc_final: 0.8653 (ttp) REVERT: 5G 107 MET cc_start: 0.8900 (ttt) cc_final: 0.8672 (ttp) REVERT: 5N 58 THR cc_start: 0.8020 (m) cc_final: 0.7749 (p) REVERT: 5N 61 ASN cc_start: 0.8111 (m-40) cc_final: 0.7702 (m-40) outliers start: 19 outliers final: 4 residues processed: 693 average time/residue: 0.2426 time to fit residues: 265.3736 Evaluate side-chains 636 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 632 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 5A residue 111 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 389 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 362 optimal weight: 0.7980 chunk 488 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 407 optimal weight: 6.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2J 73 GLN 2M 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.088130 restraints weight = 44148.556| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.83 r_work: 0.2880 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37730 Z= 0.176 Angle : 0.509 5.985 50330 Z= 0.269 Chirality : 0.037 0.121 5670 Planarity : 0.003 0.024 6020 Dihedral : 24.584 179.882 7910 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.36 % Allowed : 10.39 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.12), residues: 4760 helix: 2.06 (0.09), residues: 3990 sheet: None (None), residues: 0 loop : -1.24 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG2N 91 PHE 0.011 0.001 PHE1C 89 TRP 0.017 0.002 TRP1N 87 Details of bonding type rmsd covalent geometry : bond 0.00423 (37730) covalent geometry : angle 0.50939 (50330) hydrogen bonds : bond 0.05007 ( 2590) hydrogen bonds : angle 3.89844 ( 7770) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 632 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8186 (mtt) cc_final: 0.7887 (mtt) REVERT: 1A 73 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7477 (mm-40) REVERT: 1B 59 MET cc_start: 0.8456 (mtt) cc_final: 0.7980 (mtt) REVERT: 1C 107 MET cc_start: 0.8711 (ttt) cc_final: 0.8493 (ttp) REVERT: 1E 107 MET cc_start: 0.8927 (ttt) cc_final: 0.8647 (ttt) REVERT: 1F 107 MET cc_start: 0.8786 (ttt) cc_final: 0.8482 (ttp) REVERT: 1J 107 MET cc_start: 0.8737 (ttt) cc_final: 0.8475 (ttp) REVERT: 1L 107 MET cc_start: 0.8902 (ttt) cc_final: 0.8536 (ttt) REVERT: 1M 107 MET cc_start: 0.8502 (ttt) cc_final: 0.8170 (ttp) REVERT: 1N 61 ASN cc_start: 0.8635 (m-40) cc_final: 0.8329 (m-40) REVERT: 2A 59 MET cc_start: 0.8365 (mtt) cc_final: 0.7969 (mtt) REVERT: 2A 68 LEU cc_start: 0.8103 (mt) cc_final: 0.7822 (mt) REVERT: 2A 73 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7657 (mm-40) REVERT: 2C 108 PHE cc_start: 0.8309 (m-80) cc_final: 0.8069 (m-80) REVERT: 2E 59 MET cc_start: 0.8380 (mtt) cc_final: 0.8048 (mtt) REVERT: 2E 107 MET cc_start: 0.9026 (ttt) cc_final: 0.8794 (ttt) REVERT: 2H 107 MET cc_start: 0.9023 (ttt) cc_final: 0.8742 (ttt) REVERT: 2J 59 MET cc_start: 0.8517 (mtt) cc_final: 0.8286 (mtt) REVERT: 2L 73 GLN cc_start: 0.8786 (mt0) cc_final: 0.8458 (mm-40) REVERT: 3C 73 GLN cc_start: 0.8365 (mt0) cc_final: 0.8027 (mm-40) REVERT: 3E 107 MET cc_start: 0.8895 (ttt) cc_final: 0.8488 (ttp) REVERT: 3F 59 MET cc_start: 0.8626 (mtt) cc_final: 0.8361 (mtt) REVERT: 3G 107 MET cc_start: 0.8918 (ttt) cc_final: 0.8591 (ttp) REVERT: 3J 107 MET cc_start: 0.8752 (ttt) cc_final: 0.8513 (ttp) REVERT: 3K 107 MET cc_start: 0.8886 (ttt) cc_final: 0.8654 (ttp) REVERT: 3K 112 PHE cc_start: 0.8583 (m-80) cc_final: 0.8137 (m-80) REVERT: 3L 107 MET cc_start: 0.8763 (ttt) cc_final: 0.8394 (ttp) REVERT: 3M 107 MET cc_start: 0.8700 (ttt) cc_final: 0.8414 (ttp) REVERT: 3N 61 ASN cc_start: 0.8568 (m-40) cc_final: 0.8238 (m-40) REVERT: 3N 91 ARG cc_start: 0.7927 (tpm170) cc_final: 0.7696 (tpp-160) REVERT: 4A 73 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7616 (mm-40) REVERT: 4B 115 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7424 (ttpp) REVERT: 4H 59 MET cc_start: 0.8458 (mtt) cc_final: 0.8136 (mtt) REVERT: 4I 59 MET cc_start: 0.8434 (mtt) cc_final: 0.8086 (mtt) REVERT: 4K 59 MET cc_start: 0.8592 (mtt) cc_final: 0.8331 (mtt) REVERT: 4M 61 ASN cc_start: 0.8406 (m-40) cc_final: 0.8132 (m110) REVERT: 4M 115 LYS cc_start: 0.7942 (ttpp) cc_final: 0.7633 (ttmm) REVERT: 4N 61 ASN cc_start: 0.8318 (m-40) cc_final: 0.7953 (m-40) REVERT: 5A 108 PHE cc_start: 0.6979 (m-80) cc_final: 0.6626 (m-80) REVERT: 5I 107 MET cc_start: 0.8909 (ttt) cc_final: 0.8629 (ttp) REVERT: 5M 61 ASN cc_start: 0.8447 (m-40) cc_final: 0.8182 (m-40) REVERT: 5N 61 ASN cc_start: 0.8165 (m-40) cc_final: 0.7780 (m-40) outliers start: 12 outliers final: 9 residues processed: 638 average time/residue: 0.2603 time to fit residues: 257.7637 Evaluate side-chains 612 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 603 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1C residue 97 VAL Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 4A residue 85 ILE Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 104 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 435 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 348 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 486 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4L 61 ASN 5B 73 GLN 5L 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.091880 restraints weight = 43808.221| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.83 r_work: 0.2932 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37730 Z= 0.120 Angle : 0.432 4.909 50330 Z= 0.229 Chirality : 0.034 0.112 5670 Planarity : 0.003 0.025 6020 Dihedral : 22.081 173.287 7910 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.54 % Allowed : 11.96 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.12), residues: 4760 helix: 2.28 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.36 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG1N 91 PHE 0.009 0.001 PHE5A 112 TRP 0.010 0.002 TRP4L 87 Details of bonding type rmsd covalent geometry : bond 0.00276 (37730) covalent geometry : angle 0.43193 (50330) hydrogen bonds : bond 0.03761 ( 2590) hydrogen bonds : angle 3.57810 ( 7770) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 616 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8097 (mtt) cc_final: 0.7776 (mtt) REVERT: 1B 59 MET cc_start: 0.8481 (mtt) cc_final: 0.7966 (mtt) REVERT: 1C 107 MET cc_start: 0.8773 (ttt) cc_final: 0.8535 (ttp) REVERT: 1F 107 MET cc_start: 0.8801 (ttt) cc_final: 0.8537 (ttp) REVERT: 1J 107 MET cc_start: 0.8843 (ttt) cc_final: 0.8535 (ttp) REVERT: 1K 112 PHE cc_start: 0.8225 (m-80) cc_final: 0.7891 (m-80) REVERT: 1L 107 MET cc_start: 0.8891 (ttt) cc_final: 0.8522 (ttt) REVERT: 1M 107 MET cc_start: 0.8592 (ttt) cc_final: 0.8270 (ttt) REVERT: 1M 115 LYS cc_start: 0.8021 (ttpp) cc_final: 0.7801 (ttpp) REVERT: 1N 61 ASN cc_start: 0.8654 (m-40) cc_final: 0.8358 (m-40) REVERT: 2A 59 MET cc_start: 0.8343 (mtt) cc_final: 0.7938 (mtt) REVERT: 2A 73 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7728 (mm-40) REVERT: 2B 59 MET cc_start: 0.8176 (mtt) cc_final: 0.7955 (mtt) REVERT: 2E 107 MET cc_start: 0.9061 (ttt) cc_final: 0.8823 (ttt) REVERT: 2H 107 MET cc_start: 0.9000 (ttt) cc_final: 0.8746 (ttt) REVERT: 2I 107 MET cc_start: 0.9061 (ttt) cc_final: 0.8815 (ttp) REVERT: 2J 59 MET cc_start: 0.8470 (mtt) cc_final: 0.8238 (mtt) REVERT: 3A 73 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7530 (mm110) REVERT: 3C 73 GLN cc_start: 0.8376 (mt0) cc_final: 0.8107 (mm-40) REVERT: 3C 108 PHE cc_start: 0.8263 (m-80) cc_final: 0.8054 (m-80) REVERT: 3D 107 MET cc_start: 0.8759 (ttt) cc_final: 0.8512 (ttp) REVERT: 3E 107 MET cc_start: 0.8884 (ttt) cc_final: 0.8493 (ttp) REVERT: 3F 59 MET cc_start: 0.8510 (mtt) cc_final: 0.8308 (mtt) REVERT: 3G 107 MET cc_start: 0.8901 (ttt) cc_final: 0.8598 (ttp) REVERT: 3J 107 MET cc_start: 0.8689 (ttt) cc_final: 0.8471 (ttp) REVERT: 3K 107 MET cc_start: 0.8900 (ttt) cc_final: 0.8693 (ttp) REVERT: 3K 112 PHE cc_start: 0.8518 (m-80) cc_final: 0.8189 (m-80) REVERT: 3L 107 MET cc_start: 0.8757 (ttt) cc_final: 0.8387 (ttp) REVERT: 3M 107 MET cc_start: 0.8685 (ttt) cc_final: 0.8381 (ttp) REVERT: 3N 61 ASN cc_start: 0.8579 (m-40) cc_final: 0.8212 (m-40) REVERT: 3N 91 ARG cc_start: 0.7798 (tpm170) cc_final: 0.7535 (tpp-160) REVERT: 4A 73 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7597 (mm-40) REVERT: 4B 115 LYS cc_start: 0.7671 (mtpp) cc_final: 0.7405 (ttpp) REVERT: 4H 59 MET cc_start: 0.8461 (mtt) cc_final: 0.8124 (mtt) REVERT: 4I 59 MET cc_start: 0.8356 (mtt) cc_final: 0.7993 (mtt) REVERT: 4K 59 MET cc_start: 0.8479 (mtt) cc_final: 0.8204 (mtt) REVERT: 4L 73 GLN cc_start: 0.8639 (mt0) cc_final: 0.8185 (mm-40) REVERT: 4M 61 ASN cc_start: 0.8419 (m-40) cc_final: 0.8167 (m110) REVERT: 4N 61 ASN cc_start: 0.8293 (m-40) cc_final: 0.7939 (m-40) REVERT: 5E 107 MET cc_start: 0.8946 (ttt) cc_final: 0.8735 (ttp) REVERT: 5I 107 MET cc_start: 0.8872 (ttt) cc_final: 0.8631 (ttp) REVERT: 5M 61 ASN cc_start: 0.8382 (m-40) cc_final: 0.8135 (m-40) REVERT: 5N 61 ASN cc_start: 0.8181 (m-40) cc_final: 0.7797 (m-40) outliers start: 18 outliers final: 10 residues processed: 628 average time/residue: 0.2557 time to fit residues: 248.5265 Evaluate side-chains 595 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 585 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 463 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 453 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 339 optimal weight: 7.9990 chunk 268 optimal weight: 0.0470 chunk 123 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 73 GLN 4L 61 ASN 5L 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.088202 restraints weight = 44095.218| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.82 r_work: 0.2877 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 37730 Z= 0.161 Angle : 0.482 5.815 50330 Z= 0.256 Chirality : 0.036 0.121 5670 Planarity : 0.003 0.021 6020 Dihedral : 21.715 173.473 7910 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.77 % Allowed : 14.08 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.12), residues: 4760 helix: 2.18 (0.09), residues: 3990 sheet: None (None), residues: 0 loop : -1.59 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG3L 91 PHE 0.011 0.001 PHE4K 89 TRP 0.010 0.002 TRP5N 87 Details of bonding type rmsd covalent geometry : bond 0.00383 (37730) covalent geometry : angle 0.48184 (50330) hydrogen bonds : bond 0.04602 ( 2590) hydrogen bonds : angle 3.76731 ( 7770) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 608 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8044 (mtt) cc_final: 0.7754 (mtt) REVERT: 1A 73 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7603 (mm-40) REVERT: 1B 59 MET cc_start: 0.8476 (mtt) cc_final: 0.8004 (mtt) REVERT: 1C 107 MET cc_start: 0.8732 (ttt) cc_final: 0.8487 (ttp) REVERT: 1F 107 MET cc_start: 0.8803 (ttt) cc_final: 0.8496 (ttp) REVERT: 1J 59 MET cc_start: 0.8479 (mtt) cc_final: 0.8173 (mtt) REVERT: 1J 107 MET cc_start: 0.8752 (ttt) cc_final: 0.8462 (ttp) REVERT: 1L 107 MET cc_start: 0.8914 (ttt) cc_final: 0.8546 (ttt) REVERT: 1M 107 MET cc_start: 0.8607 (ttt) cc_final: 0.8278 (ttt) REVERT: 1M 115 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7839 (ttpp) REVERT: 1N 61 ASN cc_start: 0.8626 (m-40) cc_final: 0.8305 (m-40) REVERT: 2A 59 MET cc_start: 0.8392 (mtt) cc_final: 0.8012 (mtt) REVERT: 2A 73 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7600 (mm-40) REVERT: 2B 59 MET cc_start: 0.8322 (mtt) cc_final: 0.8007 (mtt) REVERT: 2B 115 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7794 (ttpp) REVERT: 2E 107 MET cc_start: 0.9078 (ttt) cc_final: 0.8834 (ttt) REVERT: 2H 107 MET cc_start: 0.9034 (ttt) cc_final: 0.8748 (ttt) REVERT: 2I 107 MET cc_start: 0.9066 (ttt) cc_final: 0.8807 (ttp) REVERT: 2J 59 MET cc_start: 0.8528 (mtt) cc_final: 0.8306 (mtt) REVERT: 2M 61 ASN cc_start: 0.8220 (m-40) cc_final: 0.8000 (m110) REVERT: 3A 73 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7457 (mm110) REVERT: 3B 61 ASN cc_start: 0.8231 (m-40) cc_final: 0.8001 (m110) REVERT: 3D 107 MET cc_start: 0.8768 (ttt) cc_final: 0.8510 (ttp) REVERT: 3E 107 MET cc_start: 0.8922 (ttt) cc_final: 0.8491 (ttp) REVERT: 3J 107 MET cc_start: 0.8699 (ttt) cc_final: 0.8472 (ttp) REVERT: 3L 107 MET cc_start: 0.8779 (ttt) cc_final: 0.8528 (ttp) REVERT: 3M 107 MET cc_start: 0.8724 (ttt) cc_final: 0.8419 (ttp) REVERT: 3N 61 ASN cc_start: 0.8589 (m-40) cc_final: 0.8286 (m-40) REVERT: 3N 91 ARG cc_start: 0.7763 (tpm170) cc_final: 0.7504 (tpp-160) REVERT: 4A 73 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7607 (mm-40) REVERT: 4B 115 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7535 (ttpp) REVERT: 4I 59 MET cc_start: 0.8394 (mtt) cc_final: 0.8037 (mtt) REVERT: 4K 59 MET cc_start: 0.8525 (mtt) cc_final: 0.8240 (mtt) REVERT: 4M 61 ASN cc_start: 0.8434 (m-40) cc_final: 0.8173 (m110) REVERT: 4M 115 LYS cc_start: 0.7947 (ttpp) cc_final: 0.7641 (ttmm) REVERT: 4N 61 ASN cc_start: 0.8315 (m-40) cc_final: 0.7949 (m-40) REVERT: 5B 88 MET cc_start: 0.6210 (mtm) cc_final: 0.5886 (ptp) REVERT: 5C 73 GLN cc_start: 0.8349 (mt0) cc_final: 0.8121 (mm-40) REVERT: 5I 107 MET cc_start: 0.8938 (ttt) cc_final: 0.8650 (ttp) REVERT: 5M 61 ASN cc_start: 0.8430 (m-40) cc_final: 0.8192 (m-40) REVERT: 5N 61 ASN cc_start: 0.8191 (m-40) cc_final: 0.7811 (m-40) outliers start: 26 outliers final: 21 residues processed: 628 average time/residue: 0.2565 time to fit residues: 249.4588 Evaluate side-chains 613 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 592 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1C residue 97 VAL Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1G residue 116 THR Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1L residue 115 LYS Chi-restraints excluded: chain 2C residue 88 MET Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2J residue 73 GLN Chi-restraints excluded: chain 2J residue 116 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 21 optimal weight: 10.0000 chunk 424 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 189 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 362 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2G 73 GLN 4B 73 GLN 4L 61 ASN 5L 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.088693 restraints weight = 44310.215| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.84 r_work: 0.2882 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 37730 Z= 0.158 Angle : 0.474 5.204 50330 Z= 0.251 Chirality : 0.036 0.120 5670 Planarity : 0.003 0.022 6020 Dihedral : 21.022 176.280 7910 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.74 % Allowed : 15.51 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.12), residues: 4760 helix: 2.19 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.68 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG3E 91 PHE 0.011 0.001 PHE1L 89 TRP 0.009 0.001 TRP5N 87 Details of bonding type rmsd covalent geometry : bond 0.00378 (37730) covalent geometry : angle 0.47433 (50330) hydrogen bonds : bond 0.04368 ( 2590) hydrogen bonds : angle 3.71369 ( 7770) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 603 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8073 (mtt) cc_final: 0.7753 (mtt) REVERT: 1A 73 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7628 (mm-40) REVERT: 1B 59 MET cc_start: 0.8474 (mtt) cc_final: 0.8000 (mtt) REVERT: 1C 107 MET cc_start: 0.8741 (ttt) cc_final: 0.8486 (ttp) REVERT: 1F 107 MET cc_start: 0.8804 (ttt) cc_final: 0.8507 (ttp) REVERT: 1J 107 MET cc_start: 0.8769 (ttt) cc_final: 0.8483 (ttp) REVERT: 1L 107 MET cc_start: 0.8925 (ttt) cc_final: 0.8576 (ttt) REVERT: 1M 107 MET cc_start: 0.8609 (ttt) cc_final: 0.8275 (ttt) REVERT: 1N 61 ASN cc_start: 0.8656 (m-40) cc_final: 0.8346 (m-40) REVERT: 2A 59 MET cc_start: 0.8394 (mtt) cc_final: 0.8031 (mtt) REVERT: 2A 73 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7633 (mm-40) REVERT: 2B 59 MET cc_start: 0.8340 (mtt) cc_final: 0.8032 (mtt) REVERT: 2B 115 LYS cc_start: 0.8026 (mtpp) cc_final: 0.7822 (ttpp) REVERT: 2E 107 MET cc_start: 0.9084 (ttt) cc_final: 0.8853 (ttt) REVERT: 2J 59 MET cc_start: 0.8545 (mtt) cc_final: 0.8331 (mtt) REVERT: 2M 61 ASN cc_start: 0.8248 (m-40) cc_final: 0.8045 (m110) REVERT: 2N 61 ASN cc_start: 0.8435 (m-40) cc_final: 0.8144 (m-40) REVERT: 3A 73 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7504 (mm110) REVERT: 3B 60 VAL cc_start: 0.7854 (m) cc_final: 0.7644 (m) REVERT: 3B 61 ASN cc_start: 0.8218 (m-40) cc_final: 0.8007 (m110) REVERT: 3C 73 GLN cc_start: 0.8446 (mt0) cc_final: 0.8219 (mm-40) REVERT: 3D 107 MET cc_start: 0.8778 (ttt) cc_final: 0.8531 (ttp) REVERT: 3E 107 MET cc_start: 0.8929 (ttt) cc_final: 0.8525 (ttp) REVERT: 3K 107 MET cc_start: 0.8907 (ttt) cc_final: 0.8661 (ttp) REVERT: 3L 107 MET cc_start: 0.8788 (ttt) cc_final: 0.8540 (ttp) REVERT: 3M 107 MET cc_start: 0.8705 (ttt) cc_final: 0.8396 (ttp) REVERT: 3N 61 ASN cc_start: 0.8622 (m-40) cc_final: 0.8255 (m-40) REVERT: 3N 91 ARG cc_start: 0.7685 (tpm170) cc_final: 0.7433 (tpp-160) REVERT: 4A 73 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7632 (mm-40) REVERT: 4B 115 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7542 (ttpp) REVERT: 4H 59 MET cc_start: 0.8450 (mtt) cc_final: 0.8167 (mtt) REVERT: 4I 59 MET cc_start: 0.8367 (mtt) cc_final: 0.7991 (mtt) REVERT: 4K 59 MET cc_start: 0.8539 (mtt) cc_final: 0.8248 (mtt) REVERT: 4M 61 ASN cc_start: 0.8434 (m-40) cc_final: 0.8183 (m110) REVERT: 4M 115 LYS cc_start: 0.7969 (ttpp) cc_final: 0.7664 (ttmm) REVERT: 4N 61 ASN cc_start: 0.8333 (m-40) cc_final: 0.7981 (m-40) REVERT: 5B 88 MET cc_start: 0.6208 (mtm) cc_final: 0.5822 (ptp) REVERT: 5C 73 GLN cc_start: 0.8339 (mt0) cc_final: 0.8107 (mm-40) REVERT: 5I 107 MET cc_start: 0.8928 (ttt) cc_final: 0.8651 (ttp) REVERT: 5M 61 ASN cc_start: 0.8390 (m-40) cc_final: 0.8142 (m-40) REVERT: 5N 61 ASN cc_start: 0.8188 (m-40) cc_final: 0.7824 (m-40) outliers start: 25 outliers final: 23 residues processed: 620 average time/residue: 0.2510 time to fit residues: 241.4624 Evaluate side-chains 611 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 588 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1C residue 97 VAL Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1G residue 116 THR Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1L residue 115 LYS Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2J residue 73 GLN Chi-restraints excluded: chain 2J residue 116 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 4A residue 83 ILE Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 427 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 379 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 455 optimal weight: 0.0170 chunk 240 optimal weight: 2.9990 chunk 398 optimal weight: 3.9990 chunk 387 optimal weight: 0.8980 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2B 73 GLN 3G 73 GLN 4L 61 ASN 5G 73 GLN 5L 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.090946 restraints weight = 43894.129| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.81 r_work: 0.2922 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37730 Z= 0.123 Angle : 0.436 5.493 50330 Z= 0.231 Chirality : 0.034 0.114 5670 Planarity : 0.003 0.021 6020 Dihedral : 19.872 176.845 7910 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.74 % Allowed : 16.04 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.12), residues: 4760 helix: 2.31 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.70 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG3C 91 PHE 0.010 0.001 PHE5A 112 TRP 0.008 0.001 TRP4L 87 Details of bonding type rmsd covalent geometry : bond 0.00285 (37730) covalent geometry : angle 0.43556 (50330) hydrogen bonds : bond 0.03741 ( 2590) hydrogen bonds : angle 3.52513 ( 7770) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 590 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8056 (mtt) cc_final: 0.7725 (mtt) REVERT: 1B 59 MET cc_start: 0.8464 (mtt) cc_final: 0.7982 (mtt) REVERT: 1C 73 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8047 (mm-40) REVERT: 1C 107 MET cc_start: 0.8769 (ttt) cc_final: 0.8520 (ttp) REVERT: 1F 107 MET cc_start: 0.8829 (ttt) cc_final: 0.8539 (ttp) REVERT: 1J 59 MET cc_start: 0.8408 (mtt) cc_final: 0.8084 (mtt) REVERT: 1J 107 MET cc_start: 0.8801 (ttt) cc_final: 0.8497 (ttp) REVERT: 1L 107 MET cc_start: 0.8906 (ttt) cc_final: 0.8550 (ttt) REVERT: 1M 107 MET cc_start: 0.8604 (ttt) cc_final: 0.8280 (ttt) REVERT: 1N 61 ASN cc_start: 0.8640 (m-40) cc_final: 0.8344 (m-40) REVERT: 2A 59 MET cc_start: 0.8332 (mtt) cc_final: 0.7945 (mtt) REVERT: 2A 73 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7629 (mm-40) REVERT: 2B 59 MET cc_start: 0.8250 (mtt) cc_final: 0.7931 (mtt) REVERT: 2E 107 MET cc_start: 0.9089 (ttt) cc_final: 0.8858 (ttt) REVERT: 2J 59 MET cc_start: 0.8488 (mtt) cc_final: 0.8233 (mtt) REVERT: 2M 61 ASN cc_start: 0.8218 (m-40) cc_final: 0.8016 (m-40) REVERT: 2N 61 ASN cc_start: 0.8425 (m-40) cc_final: 0.8130 (m-40) REVERT: 3A 73 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7538 (mm110) REVERT: 3B 60 VAL cc_start: 0.7749 (m) cc_final: 0.7543 (m) REVERT: 3B 61 ASN cc_start: 0.8221 (m-40) cc_final: 0.8007 (m110) REVERT: 3C 73 GLN cc_start: 0.8377 (mt0) cc_final: 0.8159 (mm-40) REVERT: 3C 91 ARG cc_start: 0.8258 (tpt170) cc_final: 0.7890 (tpt170) REVERT: 3D 107 MET cc_start: 0.8775 (ttt) cc_final: 0.8528 (ttp) REVERT: 3E 107 MET cc_start: 0.8927 (ttt) cc_final: 0.8518 (ttp) REVERT: 3K 107 MET cc_start: 0.8946 (ttt) cc_final: 0.8692 (ttp) REVERT: 3L 107 MET cc_start: 0.8904 (ttt) cc_final: 0.8655 (ttp) REVERT: 3M 107 MET cc_start: 0.8701 (ttt) cc_final: 0.8398 (ttp) REVERT: 3N 61 ASN cc_start: 0.8562 (m-40) cc_final: 0.8248 (m-40) REVERT: 3N 91 ARG cc_start: 0.7661 (tpm170) cc_final: 0.7419 (tpp-160) REVERT: 4A 73 GLN cc_start: 0.8060 (tm-30) cc_final: 0.7638 (mm-40) REVERT: 4B 115 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7532 (ttpp) REVERT: 4I 59 MET cc_start: 0.8368 (mtt) cc_final: 0.7999 (mtt) REVERT: 4K 59 MET cc_start: 0.8466 (mtt) cc_final: 0.8206 (mtt) REVERT: 4M 61 ASN cc_start: 0.8406 (m-40) cc_final: 0.8162 (m110) REVERT: 4M 115 LYS cc_start: 0.7966 (ttpp) cc_final: 0.7666 (ttmm) REVERT: 4N 61 ASN cc_start: 0.8310 (m-40) cc_final: 0.7961 (m-40) REVERT: 5B 88 MET cc_start: 0.6226 (mtm) cc_final: 0.5838 (ptp) REVERT: 5E 107 MET cc_start: 0.8991 (ttt) cc_final: 0.8771 (ttp) REVERT: 5I 107 MET cc_start: 0.8914 (ttt) cc_final: 0.8650 (ttp) REVERT: 5M 61 ASN cc_start: 0.8444 (m-40) cc_final: 0.8215 (m-40) REVERT: 5N 61 ASN cc_start: 0.8122 (m-40) cc_final: 0.7762 (m-40) outliers start: 25 outliers final: 18 residues processed: 606 average time/residue: 0.2592 time to fit residues: 243.4730 Evaluate side-chains 595 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 577 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2J residue 73 GLN Chi-restraints excluded: chain 2J residue 116 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 3M residue 116 THR Chi-restraints excluded: chain 4A residue 88 MET Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 211 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 230 optimal weight: 0.1980 chunk 199 optimal weight: 0.8980 chunk 468 optimal weight: 1.9990 chunk 458 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 329 optimal weight: 3.9990 chunk 287 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3M 61 ASN 4L 61 ASN 5L 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.089709 restraints weight = 43953.308| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.83 r_work: 0.2902 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37730 Z= 0.135 Angle : 0.454 5.453 50330 Z= 0.241 Chirality : 0.035 0.119 5670 Planarity : 0.003 0.021 6020 Dihedral : 19.447 179.823 7910 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.89 % Allowed : 16.52 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.12), residues: 4760 helix: 2.31 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.73 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG4D 91 PHE 0.011 0.001 PHE4D 89 TRP 0.010 0.001 TRP5N 87 Details of bonding type rmsd covalent geometry : bond 0.00316 (37730) covalent geometry : angle 0.45401 (50330) hydrogen bonds : bond 0.04070 ( 2590) hydrogen bonds : angle 3.60481 ( 7770) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 596 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8043 (mtt) cc_final: 0.7718 (mtt) REVERT: 1B 59 MET cc_start: 0.8498 (mtt) cc_final: 0.8016 (mtt) REVERT: 1C 73 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8084 (mm-40) REVERT: 1C 107 MET cc_start: 0.8754 (ttt) cc_final: 0.8510 (ttp) REVERT: 1F 107 MET cc_start: 0.8805 (ttt) cc_final: 0.8497 (ttp) REVERT: 1J 59 MET cc_start: 0.8410 (mtt) cc_final: 0.8115 (mtt) REVERT: 1J 107 MET cc_start: 0.8798 (ttt) cc_final: 0.8506 (ttp) REVERT: 1L 107 MET cc_start: 0.8912 (ttt) cc_final: 0.8554 (ttt) REVERT: 1M 107 MET cc_start: 0.8612 (ttt) cc_final: 0.8283 (ttt) REVERT: 1N 61 ASN cc_start: 0.8652 (m-40) cc_final: 0.8363 (m-40) REVERT: 2A 59 MET cc_start: 0.8316 (mtt) cc_final: 0.7955 (mtt) REVERT: 2A 73 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7589 (mm-40) REVERT: 2B 59 MET cc_start: 0.8269 (mtt) cc_final: 0.7953 (mtt) REVERT: 2E 107 MET cc_start: 0.9093 (ttt) cc_final: 0.8876 (ttt) REVERT: 2J 59 MET cc_start: 0.8510 (mtt) cc_final: 0.8276 (mtt) REVERT: 2M 61 ASN cc_start: 0.8222 (m-40) cc_final: 0.8018 (m-40) REVERT: 2N 61 ASN cc_start: 0.8388 (m-40) cc_final: 0.8098 (m-40) REVERT: 3A 73 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7549 (mm110) REVERT: 3B 60 VAL cc_start: 0.7748 (m) cc_final: 0.7527 (m) REVERT: 3B 61 ASN cc_start: 0.8217 (m-40) cc_final: 0.8005 (m110) REVERT: 3C 73 GLN cc_start: 0.8416 (mt0) cc_final: 0.8210 (mm-40) REVERT: 3D 107 MET cc_start: 0.8827 (ttt) cc_final: 0.8574 (ttp) REVERT: 3E 107 MET cc_start: 0.8936 (ttt) cc_final: 0.8522 (ttp) REVERT: 3K 107 MET cc_start: 0.8959 (ttt) cc_final: 0.8700 (ttp) REVERT: 3L 107 MET cc_start: 0.8814 (ttt) cc_final: 0.8571 (ttp) REVERT: 3M 61 ASN cc_start: 0.8163 (m-40) cc_final: 0.7887 (m110) REVERT: 3M 65 THR cc_start: 0.8736 (m) cc_final: 0.8377 (p) REVERT: 3M 107 MET cc_start: 0.8819 (ttt) cc_final: 0.8500 (ttp) REVERT: 3N 61 ASN cc_start: 0.8720 (m-40) cc_final: 0.8366 (m-40) REVERT: 3N 91 ARG cc_start: 0.7630 (tpm170) cc_final: 0.7380 (tpp-160) REVERT: 4A 73 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7650 (mm-40) REVERT: 4B 115 LYS cc_start: 0.7850 (mtpp) cc_final: 0.7550 (ttpp) REVERT: 4I 59 MET cc_start: 0.8404 (mtt) cc_final: 0.8043 (mtt) REVERT: 4K 59 MET cc_start: 0.8523 (mtt) cc_final: 0.8263 (mtt) REVERT: 4M 61 ASN cc_start: 0.8411 (m-40) cc_final: 0.8169 (m110) REVERT: 4M 115 LYS cc_start: 0.7910 (ttpp) cc_final: 0.7601 (ttmm) REVERT: 4N 61 ASN cc_start: 0.8324 (m-40) cc_final: 0.7975 (m-40) REVERT: 5I 107 MET cc_start: 0.8932 (ttt) cc_final: 0.8647 (ttp) REVERT: 5M 61 ASN cc_start: 0.8430 (m-40) cc_final: 0.8207 (m-40) REVERT: 5N 61 ASN cc_start: 0.8130 (m-40) cc_final: 0.7770 (m-40) outliers start: 30 outliers final: 23 residues processed: 614 average time/residue: 0.2525 time to fit residues: 240.2143 Evaluate side-chains 613 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 590 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 88 MET Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1G residue 116 THR Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2J residue 73 GLN Chi-restraints excluded: chain 2J residue 116 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3I residue 88 MET Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 4A residue 83 ILE Chi-restraints excluded: chain 4A residue 88 MET Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 433 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 228 optimal weight: 0.3980 chunk 103 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 476 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 137 optimal weight: 10.0000 chunk 426 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4L 61 ASN 5L 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.121118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.090604 restraints weight = 44151.029| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.84 r_work: 0.2917 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 37730 Z= 0.128 Angle : 0.444 5.627 50330 Z= 0.235 Chirality : 0.035 0.116 5670 Planarity : 0.003 0.021 6020 Dihedral : 18.930 177.795 7910 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.71 % Allowed : 17.08 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.12), residues: 4760 helix: 2.34 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.73 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG4D 91 PHE 0.012 0.001 PHE1A 112 TRP 0.011 0.001 TRP5N 87 Details of bonding type rmsd covalent geometry : bond 0.00297 (37730) covalent geometry : angle 0.44437 (50330) hydrogen bonds : bond 0.03816 ( 2590) hydrogen bonds : angle 3.54069 ( 7770) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 584 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8115 (mtt) cc_final: 0.7783 (mtt) REVERT: 1B 59 MET cc_start: 0.8477 (mtt) cc_final: 0.7995 (mtt) REVERT: 1C 73 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8069 (mm-40) REVERT: 1C 107 MET cc_start: 0.8756 (ttt) cc_final: 0.8510 (ttp) REVERT: 1F 107 MET cc_start: 0.8822 (ttt) cc_final: 0.8530 (ttp) REVERT: 1J 59 MET cc_start: 0.8396 (mtt) cc_final: 0.8082 (mtt) REVERT: 1J 107 MET cc_start: 0.8793 (ttt) cc_final: 0.8487 (ttp) REVERT: 1L 107 MET cc_start: 0.8897 (ttt) cc_final: 0.8538 (ttt) REVERT: 1M 107 MET cc_start: 0.8624 (ttt) cc_final: 0.8284 (ttt) REVERT: 1N 61 ASN cc_start: 0.8638 (m-40) cc_final: 0.8349 (m-40) REVERT: 2A 59 MET cc_start: 0.8311 (mtt) cc_final: 0.7942 (mtt) REVERT: 2A 73 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7660 (mm-40) REVERT: 2B 59 MET cc_start: 0.8251 (mtt) cc_final: 0.7930 (mtt) REVERT: 2E 107 MET cc_start: 0.9094 (ttt) cc_final: 0.8872 (ttt) REVERT: 2I 107 MET cc_start: 0.9074 (ttp) cc_final: 0.8827 (ttp) REVERT: 2J 59 MET cc_start: 0.8468 (mtt) cc_final: 0.8236 (mtt) REVERT: 2M 61 ASN cc_start: 0.8211 (m-40) cc_final: 0.7998 (m-40) REVERT: 2N 61 ASN cc_start: 0.8376 (m-40) cc_final: 0.8090 (m-40) REVERT: 3A 73 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7578 (mm110) REVERT: 3B 60 VAL cc_start: 0.7739 (m) cc_final: 0.7529 (m) REVERT: 3B 61 ASN cc_start: 0.8240 (m-40) cc_final: 0.8021 (m110) REVERT: 3D 107 MET cc_start: 0.8796 (ttt) cc_final: 0.8545 (ttp) REVERT: 3E 107 MET cc_start: 0.8939 (ttt) cc_final: 0.8532 (ttp) REVERT: 3K 107 MET cc_start: 0.8967 (ttt) cc_final: 0.8706 (ttp) REVERT: 3L 107 MET cc_start: 0.8900 (ttt) cc_final: 0.8652 (ttp) REVERT: 3M 61 ASN cc_start: 0.7902 (m-40) cc_final: 0.7572 (m110) REVERT: 3M 65 THR cc_start: 0.8722 (m) cc_final: 0.8361 (p) REVERT: 3M 107 MET cc_start: 0.8798 (ttt) cc_final: 0.8483 (ttp) REVERT: 3N 61 ASN cc_start: 0.8547 (m-40) cc_final: 0.8249 (m-40) REVERT: 3N 91 ARG cc_start: 0.7696 (tpm170) cc_final: 0.7467 (tpp-160) REVERT: 4A 73 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7642 (mm-40) REVERT: 4B 115 LYS cc_start: 0.7848 (mtpp) cc_final: 0.7564 (ttpp) REVERT: 4I 59 MET cc_start: 0.8416 (mtt) cc_final: 0.8077 (mtt) REVERT: 4K 59 MET cc_start: 0.8498 (mtt) cc_final: 0.8247 (mtt) REVERT: 4M 61 ASN cc_start: 0.8402 (m-40) cc_final: 0.8165 (m110) REVERT: 4M 115 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7592 (ttmm) REVERT: 4N 61 ASN cc_start: 0.8306 (m-40) cc_final: 0.7970 (m-40) REVERT: 5B 88 MET cc_start: 0.6269 (mtm) cc_final: 0.5795 (ptp) REVERT: 5E 107 MET cc_start: 0.9000 (ttt) cc_final: 0.8775 (ttp) REVERT: 5I 107 MET cc_start: 0.8917 (ttt) cc_final: 0.8647 (ttp) REVERT: 5M 61 ASN cc_start: 0.8448 (m-40) cc_final: 0.8222 (m-40) REVERT: 5N 61 ASN cc_start: 0.8108 (m-40) cc_final: 0.7758 (m-40) outliers start: 24 outliers final: 23 residues processed: 599 average time/residue: 0.2559 time to fit residues: 237.4000 Evaluate side-chains 602 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 579 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 88 MET Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1G residue 116 THR Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2J residue 73 GLN Chi-restraints excluded: chain 2J residue 116 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 116 THR Chi-restraints excluded: chain 4A residue 88 MET Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5K residue 107 MET Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 304 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 297 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 414 optimal weight: 6.9990 chunk 368 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 305 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1B 73 GLN 2H 73 GLN 4H 73 GLN 4L 61 ASN 5L 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.092813 restraints weight = 43706.391| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.84 r_work: 0.2949 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 37730 Z= 0.107 Angle : 0.424 4.924 50330 Z= 0.224 Chirality : 0.034 0.116 5670 Planarity : 0.003 0.021 6020 Dihedral : 18.102 166.951 7910 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.60 % Allowed : 17.20 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.12), residues: 4760 helix: 2.44 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.71 (0.16), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG5E 91 PHE 0.013 0.001 PHE5A 112 TRP 0.009 0.001 TRP5N 87 Details of bonding type rmsd covalent geometry : bond 0.00242 (37730) covalent geometry : angle 0.42439 (50330) hydrogen bonds : bond 0.03418 ( 2590) hydrogen bonds : angle 3.42109 ( 7770) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 591 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8070 (mtt) cc_final: 0.7716 (mtt) REVERT: 1B 59 MET cc_start: 0.8476 (mtt) cc_final: 0.7990 (mtt) REVERT: 1C 73 GLN cc_start: 0.8352 (mm-40) cc_final: 0.8017 (mm-40) REVERT: 1C 107 MET cc_start: 0.8756 (ttt) cc_final: 0.8511 (ttp) REVERT: 1F 107 MET cc_start: 0.8827 (ttt) cc_final: 0.8559 (ttp) REVERT: 1J 59 MET cc_start: 0.8385 (mtt) cc_final: 0.8054 (mtt) REVERT: 1J 107 MET cc_start: 0.8788 (ttt) cc_final: 0.8477 (ttp) REVERT: 1K 112 PHE cc_start: 0.8172 (m-80) cc_final: 0.7847 (m-80) REVERT: 1L 107 MET cc_start: 0.8876 (ttt) cc_final: 0.8512 (ttt) REVERT: 1M 107 MET cc_start: 0.8586 (ttt) cc_final: 0.8260 (ttt) REVERT: 1N 61 ASN cc_start: 0.8587 (m-40) cc_final: 0.8200 (m-40) REVERT: 2A 59 MET cc_start: 0.8273 (mtt) cc_final: 0.7915 (mtt) REVERT: 2A 73 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7639 (mm-40) REVERT: 2B 59 MET cc_start: 0.8216 (mtt) cc_final: 0.7902 (mtt) REVERT: 2E 107 MET cc_start: 0.9081 (ttt) cc_final: 0.8864 (ttt) REVERT: 2J 59 MET cc_start: 0.8432 (mtt) cc_final: 0.8192 (mtt) REVERT: 2M 61 ASN cc_start: 0.8228 (m-40) cc_final: 0.8013 (m-40) REVERT: 2N 61 ASN cc_start: 0.8356 (m-40) cc_final: 0.8081 (m-40) REVERT: 3A 73 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7574 (mm110) REVERT: 3B 60 VAL cc_start: 0.7626 (m) cc_final: 0.7420 (m) REVERT: 3C 73 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8026 (mm-40) REVERT: 3D 107 MET cc_start: 0.8798 (ttt) cc_final: 0.8551 (ttp) REVERT: 3E 107 MET cc_start: 0.8935 (ttt) cc_final: 0.8536 (ttp) REVERT: 3K 107 MET cc_start: 0.8959 (ttt) cc_final: 0.8705 (ttp) REVERT: 3L 107 MET cc_start: 0.8899 (ttt) cc_final: 0.8649 (ttp) REVERT: 3M 61 ASN cc_start: 0.7970 (m-40) cc_final: 0.7707 (m-40) REVERT: 3M 65 THR cc_start: 0.8705 (m) cc_final: 0.8357 (p) REVERT: 3M 107 MET cc_start: 0.8781 (ttt) cc_final: 0.8471 (ttp) REVERT: 3N 59 MET cc_start: 0.7882 (mtp) cc_final: 0.7637 (mtt) REVERT: 3N 61 ASN cc_start: 0.8677 (m-40) cc_final: 0.8342 (m-40) REVERT: 3N 91 ARG cc_start: 0.7662 (tpm170) cc_final: 0.7440 (tpp-160) REVERT: 4A 73 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7625 (mm-40) REVERT: 4B 115 LYS cc_start: 0.7856 (mtpp) cc_final: 0.7572 (ttpp) REVERT: 4I 59 MET cc_start: 0.8377 (mtt) cc_final: 0.8025 (mtt) REVERT: 4K 59 MET cc_start: 0.8450 (mtt) cc_final: 0.8212 (mtt) REVERT: 4L 73 GLN cc_start: 0.8711 (mt0) cc_final: 0.8495 (mm-40) REVERT: 4M 61 ASN cc_start: 0.8368 (m-40) cc_final: 0.8137 (m110) REVERT: 4M 115 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7611 (ttmm) REVERT: 4N 61 ASN cc_start: 0.8276 (m-40) cc_final: 0.7946 (m-40) REVERT: 5B 88 MET cc_start: 0.6114 (mtm) cc_final: 0.5667 (ptp) REVERT: 5E 91 ARG cc_start: 0.8622 (tpt170) cc_final: 0.8324 (tpp80) REVERT: 5E 107 MET cc_start: 0.9001 (ttt) cc_final: 0.8794 (ttp) REVERT: 5I 107 MET cc_start: 0.8902 (ttt) cc_final: 0.8634 (ttp) REVERT: 5M 61 ASN cc_start: 0.8424 (m-40) cc_final: 0.8204 (m-40) REVERT: 5N 61 ASN cc_start: 0.8120 (m-40) cc_final: 0.7777 (m-40) outliers start: 20 outliers final: 20 residues processed: 602 average time/residue: 0.2569 time to fit residues: 238.3638 Evaluate side-chains 598 residues out of total 3360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 578 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 88 MET Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2J residue 73 GLN Chi-restraints excluded: chain 2J residue 116 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 116 THR Chi-restraints excluded: chain 4A residue 83 ILE Chi-restraints excluded: chain 4A residue 88 MET Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5K residue 107 MET Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 358 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 177 optimal weight: 0.6980 chunk 260 optimal weight: 6.9990 chunk 275 optimal weight: 0.9990 chunk 424 optimal weight: 0.9980 chunk 278 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 459 optimal weight: 8.9990 chunk 347 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 61 ASN 5L 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.092949 restraints weight = 43659.148| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.84 r_work: 0.2952 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 37730 Z= 0.108 Angle : 0.426 4.992 50330 Z= 0.224 Chirality : 0.034 0.117 5670 Planarity : 0.003 0.021 6020 Dihedral : 17.566 138.642 7910 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.54 % Allowed : 17.50 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.12), residues: 4760 helix: 2.48 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.71 (0.16), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG1C 91 PHE 0.013 0.001 PHE5A 112 TRP 0.009 0.001 TRP5N 87 Details of bonding type rmsd covalent geometry : bond 0.00243 (37730) covalent geometry : angle 0.42579 (50330) hydrogen bonds : bond 0.03463 ( 2590) hydrogen bonds : angle 3.40934 ( 7770) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9029.77 seconds wall clock time: 154 minutes 20.41 seconds (9260.41 seconds total)