Starting phenix.real_space_refine on Tue Aug 26 16:31:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s6h_19758/08_2025/8s6h_19758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s6h_19758/08_2025/8s6h_19758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s6h_19758/08_2025/8s6h_19758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s6h_19758/08_2025/8s6h_19758.map" model { file = "/net/cci-nas-00/data/ceres_data/8s6h_19758/08_2025/8s6h_19758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s6h_19758/08_2025/8s6h_19758.cif" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.086 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 69 5.49 5 S 138 5.16 5 C 26013 2.51 5 N 5865 2.21 5 O 7107 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39192 Number of models: 1 Model: "" Number of chains: 121 Chain: "A" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "B" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "C" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "D" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "E" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "F" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "G" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "H" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "I" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "J" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "K" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "L" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "M" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "N" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "3" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "4" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "5" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "6" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "7" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "8" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "9" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A1" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A2" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A3" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A4" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A5" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A6" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A7" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "0" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "1" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "2" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "p" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "q" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "r" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "s" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "t" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "u" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "v" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "x" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "y" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "z" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "c" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "d" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "e" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "f" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "g" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "h" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "i" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "j" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "k" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "l" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "m" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "n" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "o" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "O" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "P" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "Q" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "R" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "S" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "T" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "U" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "V" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "W" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "X" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "Y" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "Z" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "a" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "b" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 519 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "A1" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "A2" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A3" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "A4" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "A5" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "A6" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "d" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.42, per 1000 atoms: 0.27 Number of scatterers: 39192 At special positions: 0 Unit cell: (103.499, 103.499, 244.343, 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 138 16.00 P 69 15.00 O 7107 8.00 N 5865 7.00 C 26013 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: 3.23 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8832 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 0 sheets defined 89.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 47 through 82 Proline residue: A 66 - end of helix Processing helix chain 'A' and resid 87 through 102 removed outlier: 4.063A pdb=" N VAL A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'B' and resid 47 through 82 Proline residue: B 66 - end of helix removed outlier: 3.542A pdb=" N ILE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 removed outlier: 4.103A pdb=" N VAL B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'C' and resid 47 through 82 Proline residue: C 66 - end of helix removed outlier: 3.532A pdb=" N ILE C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 removed outlier: 4.192A pdb=" N VAL C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'D' and resid 47 through 82 Proline residue: D 66 - end of helix removed outlier: 3.595A pdb=" N ILE D 78 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 102 removed outlier: 4.080A pdb=" N VAL D 91 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'E' and resid 47 through 82 Proline residue: E 66 - end of helix removed outlier: 3.563A pdb=" N ILE E 78 " --> pdb=" O LEU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 102 removed outlier: 4.155A pdb=" N VAL E 91 " --> pdb=" O LYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 111 Processing helix chain 'F' and resid 47 through 82 Proline residue: F 66 - end of helix Processing helix chain 'F' and resid 87 through 102 removed outlier: 4.167A pdb=" N VAL F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'G' and resid 47 through 82 Proline residue: G 66 - end of helix Processing helix chain 'G' and resid 87 through 102 removed outlier: 4.080A pdb=" N VAL G 91 " --> pdb=" O LYS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 111 Processing helix chain 'H' and resid 47 through 82 Proline residue: H 66 - end of helix removed outlier: 3.516A pdb=" N ILE H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 removed outlier: 4.224A pdb=" N VAL H 91 " --> pdb=" O LYS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'I' and resid 47 through 82 Proline residue: I 66 - end of helix removed outlier: 3.532A pdb=" N ILE I 78 " --> pdb=" O LEU I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 102 removed outlier: 4.209A pdb=" N VAL I 91 " --> pdb=" O LYS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 111 Processing helix chain 'J' and resid 47 through 82 Proline residue: J 66 - end of helix removed outlier: 3.564A pdb=" N ILE J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 102 removed outlier: 4.240A pdb=" N VAL J 91 " --> pdb=" O LYS J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 111 Processing helix chain 'K' and resid 47 through 82 Proline residue: K 66 - end of helix removed outlier: 3.507A pdb=" N ILE K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 102 removed outlier: 4.181A pdb=" N VAL K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 111 Processing helix chain 'L' and resid 47 through 82 Proline residue: L 66 - end of helix removed outlier: 3.546A pdb=" N ILE L 78 " --> pdb=" O LEU L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 102 removed outlier: 4.189A pdb=" N VAL L 91 " --> pdb=" O LYS L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 111 Processing helix chain 'M' and resid 47 through 82 Proline residue: M 66 - end of helix removed outlier: 3.574A pdb=" N ILE M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 102 removed outlier: 4.222A pdb=" N VAL M 91 " --> pdb=" O LYS M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 111 Processing helix chain 'N' and resid 47 through 82 Proline residue: N 66 - end of helix removed outlier: 3.522A pdb=" N ILE N 78 " --> pdb=" O LEU N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 102 removed outlier: 4.074A pdb=" N VAL N 91 " --> pdb=" O LYS N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 111 Processing helix chain '3' and resid 47 through 82 Proline residue: 3 66 - end of helix Processing helix chain '3' and resid 87 through 102 removed outlier: 4.054A pdb=" N VAL 3 91 " --> pdb=" O LYS 3 87 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 111 Processing helix chain '4' and resid 47 through 82 Proline residue: 4 66 - end of helix Processing helix chain '4' and resid 87 through 102 removed outlier: 4.086A pdb=" N VAL 4 91 " --> pdb=" O LYS 4 87 " (cutoff:3.500A) Processing helix chain '4' and resid 102 through 111 Processing helix chain '5' and resid 47 through 82 Proline residue: 5 66 - end of helix Processing helix chain '5' and resid 87 through 102 removed outlier: 4.145A pdb=" N VAL 5 91 " --> pdb=" O LYS 5 87 " (cutoff:3.500A) Processing helix chain '5' and resid 102 through 111 Processing helix chain '6' and resid 47 through 82 Proline residue: 6 66 - end of helix removed outlier: 3.503A pdb=" N ILE 6 78 " --> pdb=" O LEU 6 74 " (cutoff:3.500A) Processing helix chain '6' and resid 87 through 102 removed outlier: 4.229A pdb=" N VAL 6 91 " --> pdb=" O LYS 6 87 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 111 Processing helix chain '7' and resid 47 through 82 Proline residue: 7 66 - end of helix Processing helix chain '7' and resid 87 through 102 removed outlier: 4.121A pdb=" N VAL 7 91 " --> pdb=" O LYS 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 111 Processing helix chain '8' and resid 47 through 82 Proline residue: 8 66 - end of helix removed outlier: 3.560A pdb=" N ILE 8 78 " --> pdb=" O LEU 8 74 " (cutoff:3.500A) Processing helix chain '8' and resid 87 through 102 removed outlier: 4.145A pdb=" N VAL 8 91 " --> pdb=" O LYS 8 87 " (cutoff:3.500A) Processing helix chain '8' and resid 102 through 111 Processing helix chain '9' and resid 47 through 82 Proline residue: 9 66 - end of helix Processing helix chain '9' and resid 87 through 102 removed outlier: 4.128A pdb=" N VAL 9 91 " --> pdb=" O LYS 9 87 " (cutoff:3.500A) Processing helix chain '9' and resid 102 through 111 Processing helix chain 'A1' and resid 47 through 82 Proline residue: A1 66 - end of helix Processing helix chain 'A1' and resid 87 through 102 removed outlier: 4.074A pdb=" N VALA1 91 " --> pdb=" O LYSA1 87 " (cutoff:3.500A) Processing helix chain 'A1' and resid 102 through 111 Processing helix chain 'A2' and resid 47 through 82 Proline residue: A2 66 - end of helix Processing helix chain 'A2' and resid 87 through 102 removed outlier: 4.158A pdb=" N VALA2 91 " --> pdb=" O LYSA2 87 " (cutoff:3.500A) Processing helix chain 'A2' and resid 102 through 111 Processing helix chain 'A3' and resid 47 through 82 Proline residue: A3 66 - end of helix Processing helix chain 'A3' and resid 87 through 102 removed outlier: 4.115A pdb=" N VALA3 91 " --> pdb=" O LYSA3 87 " (cutoff:3.500A) Processing helix chain 'A3' and resid 102 through 111 Processing helix chain 'A4' and resid 47 through 82 Proline residue: A4 66 - end of helix Processing helix chain 'A4' and resid 87 through 102 removed outlier: 4.101A pdb=" N VALA4 91 " --> pdb=" O LYSA4 87 " (cutoff:3.500A) Processing helix chain 'A4' and resid 102 through 111 Processing helix chain 'A5' and resid 47 through 82 Proline residue: A5 66 - end of helix Processing helix chain 'A5' and resid 87 through 102 removed outlier: 4.173A pdb=" N VALA5 91 " --> pdb=" O LYSA5 87 " (cutoff:3.500A) Processing helix chain 'A5' and resid 102 through 111 Processing helix chain 'A6' and resid 47 through 82 Proline residue: A6 66 - end of helix removed outlier: 3.536A pdb=" N ILEA6 78 " --> pdb=" O LEUA6 74 " (cutoff:3.500A) Processing helix chain 'A6' and resid 87 through 102 removed outlier: 4.171A pdb=" N VALA6 91 " --> pdb=" O LYSA6 87 " (cutoff:3.500A) Processing helix chain 'A6' and resid 102 through 111 Processing helix chain 'A7' and resid 47 through 82 Proline residue: A7 66 - end of helix Processing helix chain 'A7' and resid 87 through 102 removed outlier: 4.151A pdb=" N VALA7 91 " --> pdb=" O LYSA7 87 " (cutoff:3.500A) Processing helix chain 'A7' and resid 102 through 111 Processing helix chain '0' and resid 47 through 82 Proline residue: 0 66 - end of helix removed outlier: 3.509A pdb=" N ILE 0 78 " --> pdb=" O LEU 0 74 " (cutoff:3.500A) Processing helix chain '0' and resid 87 through 102 removed outlier: 4.061A pdb=" N VAL 0 91 " --> pdb=" O LYS 0 87 " (cutoff:3.500A) Processing helix chain '0' and resid 102 through 111 Processing helix chain '1' and resid 47 through 82 Proline residue: 1 66 - end of helix removed outlier: 3.531A pdb=" N ILE 1 78 " --> pdb=" O LEU 1 74 " (cutoff:3.500A) Processing helix chain '1' and resid 87 through 102 removed outlier: 4.153A pdb=" N VAL 1 91 " --> pdb=" O LYS 1 87 " (cutoff:3.500A) Processing helix chain '1' and resid 102 through 111 Processing helix chain '2' and resid 47 through 82 Proline residue: 2 66 - end of helix removed outlier: 3.511A pdb=" N ILE 2 78 " --> pdb=" O LEU 2 74 " (cutoff:3.500A) Processing helix chain '2' and resid 87 through 102 removed outlier: 4.116A pdb=" N VAL 2 91 " --> pdb=" O LYS 2 87 " (cutoff:3.500A) Processing helix chain '2' and resid 102 through 111 Processing helix chain 'p' and resid 47 through 82 Proline residue: p 66 - end of helix removed outlier: 3.533A pdb=" N ILE p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) Processing helix chain 'p' and resid 87 through 102 removed outlier: 4.072A pdb=" N VAL p 91 " --> pdb=" O LYS p 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 111 Processing helix chain 'q' and resid 47 through 82 Proline residue: q 66 - end of helix removed outlier: 3.529A pdb=" N ILE q 78 " --> pdb=" O LEU q 74 " (cutoff:3.500A) Processing helix chain 'q' and resid 87 through 102 removed outlier: 4.053A pdb=" N VAL q 91 " --> pdb=" O LYS q 87 " (cutoff:3.500A) Processing helix chain 'q' and resid 102 through 111 Processing helix chain 'r' and resid 47 through 82 Proline residue: r 66 - end of helix removed outlier: 3.558A pdb=" N ILE r 78 " --> pdb=" O LEU r 74 " (cutoff:3.500A) Processing helix chain 'r' and resid 87 through 102 removed outlier: 4.075A pdb=" N VAL r 91 " --> pdb=" O LYS r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 102 through 111 Processing helix chain 's' and resid 47 through 82 Proline residue: s 66 - end of helix removed outlier: 3.538A pdb=" N ILE s 78 " --> pdb=" O LEU s 74 " (cutoff:3.500A) Processing helix chain 's' and resid 87 through 102 removed outlier: 4.093A pdb=" N VAL s 91 " --> pdb=" O LYS s 87 " (cutoff:3.500A) Processing helix chain 's' and resid 102 through 111 Processing helix chain 't' and resid 47 through 82 Proline residue: t 66 - end of helix removed outlier: 3.546A pdb=" N ILE t 78 " --> pdb=" O LEU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 87 through 102 removed outlier: 4.179A pdb=" N VAL t 91 " --> pdb=" O LYS t 87 " (cutoff:3.500A) Processing helix chain 't' and resid 102 through 111 Processing helix chain 'u' and resid 47 through 82 Proline residue: u 66 - end of helix removed outlier: 3.505A pdb=" N ILE u 78 " --> pdb=" O LEU u 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 87 through 102 removed outlier: 4.141A pdb=" N VAL u 91 " --> pdb=" O LYS u 87 " (cutoff:3.500A) Processing helix chain 'u' and resid 102 through 111 Processing helix chain 'v' and resid 47 through 82 Proline residue: v 66 - end of helix removed outlier: 3.529A pdb=" N ILE v 78 " --> pdb=" O LEU v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 87 through 102 removed outlier: 4.095A pdb=" N VAL v 91 " --> pdb=" O LYS v 87 " (cutoff:3.500A) Processing helix chain 'v' and resid 102 through 111 Processing helix chain 'w' and resid 47 through 82 Proline residue: w 66 - end of helix removed outlier: 3.524A pdb=" N ILE w 78 " --> pdb=" O LEU w 74 " (cutoff:3.500A) Processing helix chain 'w' and resid 87 through 102 removed outlier: 4.105A pdb=" N VAL w 91 " --> pdb=" O LYS w 87 " (cutoff:3.500A) Processing helix chain 'w' and resid 102 through 111 Processing helix chain 'x' and resid 47 through 82 Proline residue: x 66 - end of helix removed outlier: 3.577A pdb=" N ILE x 78 " --> pdb=" O LEU x 74 " (cutoff:3.500A) Processing helix chain 'x' and resid 87 through 102 removed outlier: 4.020A pdb=" N VAL x 91 " --> pdb=" O LYS x 87 " (cutoff:3.500A) Processing helix chain 'x' and resid 102 through 111 Processing helix chain 'y' and resid 47 through 82 Proline residue: y 66 - end of helix removed outlier: 3.527A pdb=" N ILE y 78 " --> pdb=" O LEU y 74 " (cutoff:3.500A) Processing helix chain 'y' and resid 87 through 102 removed outlier: 4.089A pdb=" N VAL y 91 " --> pdb=" O LYS y 87 " (cutoff:3.500A) Processing helix chain 'y' and resid 102 through 111 Processing helix chain 'z' and resid 47 through 82 Proline residue: z 66 - end of helix Processing helix chain 'z' and resid 87 through 102 removed outlier: 4.067A pdb=" N VAL z 91 " --> pdb=" O LYS z 87 " (cutoff:3.500A) Processing helix chain 'z' and resid 102 through 111 Processing helix chain 'c' and resid 47 through 82 Proline residue: c 66 - end of helix Processing helix chain 'c' and resid 87 through 102 removed outlier: 4.129A pdb=" N VAL c 91 " --> pdb=" O LYS c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 102 through 111 Processing helix chain 'd' and resid 47 through 82 Proline residue: d 66 - end of helix Processing helix chain 'd' and resid 87 through 102 removed outlier: 4.073A pdb=" N VAL d 91 " --> pdb=" O LYS d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 111 Processing helix chain 'e' and resid 47 through 82 Proline residue: e 66 - end of helix Processing helix chain 'e' and resid 87 through 102 removed outlier: 4.059A pdb=" N VAL e 91 " --> pdb=" O LYS e 87 " (cutoff:3.500A) Processing helix chain 'e' and resid 102 through 111 Processing helix chain 'f' and resid 47 through 82 Proline residue: f 66 - end of helix removed outlier: 3.555A pdb=" N ILE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 87 through 102 removed outlier: 4.047A pdb=" N VAL f 91 " --> pdb=" O LYS f 87 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 111 Processing helix chain 'g' and resid 47 through 82 Proline residue: g 66 - end of helix removed outlier: 3.539A pdb=" N ILE g 78 " --> pdb=" O LEU g 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 102 removed outlier: 4.165A pdb=" N VAL g 91 " --> pdb=" O LYS g 87 " (cutoff:3.500A) Processing helix chain 'g' and resid 102 through 111 Processing helix chain 'h' and resid 47 through 82 Proline residue: h 66 - end of helix Processing helix chain 'h' and resid 87 through 102 removed outlier: 4.119A pdb=" N VAL h 91 " --> pdb=" O LYS h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 111 Processing helix chain 'i' and resid 47 through 82 Proline residue: i 66 - end of helix Processing helix chain 'i' and resid 87 through 102 removed outlier: 4.049A pdb=" N VAL i 91 " --> pdb=" O LYS i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 102 through 111 Processing helix chain 'j' and resid 47 through 82 Proline residue: j 66 - end of helix Processing helix chain 'j' and resid 87 through 102 removed outlier: 4.150A pdb=" N VAL j 91 " --> pdb=" O LYS j 87 " (cutoff:3.500A) Processing helix chain 'j' and resid 102 through 111 Processing helix chain 'k' and resid 47 through 82 Proline residue: k 66 - end of helix removed outlier: 3.529A pdb=" N ILE k 78 " --> pdb=" O LEU k 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 102 removed outlier: 4.167A pdb=" N VAL k 91 " --> pdb=" O LYS k 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 102 through 111 Processing helix chain 'l' and resid 47 through 82 Proline residue: l 66 - end of helix removed outlier: 3.526A pdb=" N ILE l 78 " --> pdb=" O LEU l 74 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 102 removed outlier: 4.164A pdb=" N VAL l 91 " --> pdb=" O LYS l 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 102 through 111 Processing helix chain 'm' and resid 47 through 82 Proline residue: m 66 - end of helix removed outlier: 3.537A pdb=" N ILE m 78 " --> pdb=" O LEU m 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 102 removed outlier: 4.123A pdb=" N VAL m 91 " --> pdb=" O LYS m 87 " (cutoff:3.500A) Processing helix chain 'm' and resid 102 through 111 Processing helix chain 'n' and resid 47 through 82 Proline residue: n 66 - end of helix Processing helix chain 'n' and resid 87 through 102 removed outlier: 4.085A pdb=" N VAL n 91 " --> pdb=" O LYS n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 102 through 111 Processing helix chain 'o' and resid 47 through 82 Proline residue: o 66 - end of helix Processing helix chain 'o' and resid 87 through 102 removed outlier: 4.151A pdb=" N VAL o 91 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 102 through 111 Processing helix chain 'O' and resid 47 through 82 Proline residue: O 66 - end of helix removed outlier: 3.529A pdb=" N ILE O 78 " --> pdb=" O LEU O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 102 removed outlier: 4.126A pdb=" N VAL O 91 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 111 Processing helix chain 'P' and resid 47 through 82 Proline residue: P 66 - end of helix removed outlier: 3.535A pdb=" N ILE P 78 " --> pdb=" O LEU P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 102 removed outlier: 4.201A pdb=" N VAL P 91 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 111 Processing helix chain 'Q' and resid 47 through 82 Proline residue: Q 66 - end of helix removed outlier: 3.520A pdb=" N ILE Q 78 " --> pdb=" O LEU Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 102 removed outlier: 4.117A pdb=" N VAL Q 91 " --> pdb=" O LYS Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 111 Processing helix chain 'R' and resid 47 through 82 Proline residue: R 66 - end of helix Processing helix chain 'R' and resid 87 through 102 removed outlier: 4.134A pdb=" N VAL R 91 " --> pdb=" O LYS R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 111 Processing helix chain 'S' and resid 47 through 82 Proline residue: S 66 - end of helix Processing helix chain 'S' and resid 87 through 102 removed outlier: 4.101A pdb=" N VAL S 91 " --> pdb=" O LYS S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 111 Processing helix chain 'T' and resid 47 through 82 Proline residue: T 66 - end of helix removed outlier: 3.509A pdb=" N ILE T 78 " --> pdb=" O LEU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 102 removed outlier: 4.143A pdb=" N VAL T 91 " --> pdb=" O LYS T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 111 Processing helix chain 'U' and resid 47 through 82 Proline residue: U 66 - end of helix removed outlier: 3.545A pdb=" N ILE U 78 " --> pdb=" O LEU U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 102 removed outlier: 4.156A pdb=" N VAL U 91 " --> pdb=" O LYS U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 111 Processing helix chain 'V' and resid 47 through 82 Proline residue: V 66 - end of helix removed outlier: 3.561A pdb=" N ILE V 78 " --> pdb=" O LEU V 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 102 removed outlier: 4.093A pdb=" N VAL V 91 " --> pdb=" O LYS V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 111 Processing helix chain 'W' and resid 47 through 82 Proline residue: W 66 - end of helix removed outlier: 3.551A pdb=" N ILE W 78 " --> pdb=" O LEU W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 87 through 102 removed outlier: 4.184A pdb=" N VAL W 91 " --> pdb=" O LYS W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 111 Processing helix chain 'X' and resid 47 through 82 Proline residue: X 66 - end of helix Processing helix chain 'X' and resid 87 through 102 removed outlier: 4.137A pdb=" N VAL X 91 " --> pdb=" O LYS X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 111 Processing helix chain 'Y' and resid 47 through 82 Proline residue: Y 66 - end of helix Processing helix chain 'Y' and resid 87 through 102 removed outlier: 4.140A pdb=" N VAL Y 91 " --> pdb=" O LYS Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 102 through 111 Processing helix chain 'Z' and resid 47 through 82 Proline residue: Z 66 - end of helix Processing helix chain 'Z' and resid 87 through 102 removed outlier: 4.111A pdb=" N VAL Z 91 " --> pdb=" O LYS Z 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 111 Processing helix chain 'a' and resid 47 through 82 Proline residue: a 66 - end of helix Processing helix chain 'a' and resid 87 through 102 removed outlier: 4.050A pdb=" N VAL a 91 " --> pdb=" O LYS a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 111 Processing helix chain 'b' and resid 47 through 82 Proline residue: b 66 - end of helix removed outlier: 3.535A pdb=" N ILE b 78 " --> pdb=" O LEU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 102 removed outlier: 4.109A pdb=" N VAL b 91 " --> pdb=" O LYS b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 111 3134 hydrogen bonds defined for protein. 9402 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: 6.62 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 5865 1.30 - 1.43: 8487 1.43 - 1.55: 22645 1.55 - 1.68: 2195 1.68 - 1.81: 345 Bond restraints: 39537 Sorted by residual: bond pdb=" C7 LHG c 201 " pdb=" O7 LHG c 201 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C7 LHG Y 201 " pdb=" O7 LHG Y 201 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C7 LHGA6 202 " pdb=" O7 LHGA6 202 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C7 LHG X 201 " pdb=" O7 LHG X 201 " ideal model delta sigma weight residual 1.329 1.453 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C7 LHG z 201 " pdb=" O7 LHG z 201 " ideal model delta sigma weight residual 1.329 1.452 -0.123 2.00e-02 2.50e+03 3.81e+01 ... (remaining 39532 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 50153 1.75 - 3.51: 1947 3.51 - 5.26: 524 5.26 - 7.01: 230 7.01 - 8.76: 69 Bond angle restraints: 52923 Sorted by residual: angle pdb=" O3 LHG M 201 " pdb=" P LHG M 201 " pdb=" O6 LHG M 201 " ideal model delta sigma weight residual 97.63 106.39 -8.76 3.00e+00 1.11e-01 8.53e+00 angle pdb=" O3 LHG W 202 " pdb=" P LHG W 202 " pdb=" O6 LHG W 202 " ideal model delta sigma weight residual 97.63 106.18 -8.55 3.00e+00 1.11e-01 8.13e+00 angle pdb=" O3 LHG S 202 " pdb=" P LHG S 202 " pdb=" O6 LHG S 202 " ideal model delta sigma weight residual 97.63 106.08 -8.45 3.00e+00 1.11e-01 7.94e+00 angle pdb=" O3 LHG 5 201 " pdb=" P LHG 5 201 " pdb=" O6 LHG 5 201 " ideal model delta sigma weight residual 97.63 106.07 -8.44 3.00e+00 1.11e-01 7.91e+00 angle pdb=" O3 LHG j 202 " pdb=" P LHG j 202 " pdb=" O6 LHG j 202 " ideal model delta sigma weight residual 97.63 106.05 -8.42 3.00e+00 1.11e-01 7.88e+00 ... (remaining 52918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 21319 17.71 - 35.41: 2224 35.41 - 53.12: 811 53.12 - 70.83: 266 70.83 - 88.53: 13 Dihedral angle restraints: 24633 sinusoidal: 11040 harmonic: 13593 Sorted by residual: dihedral pdb=" CB ARGA5 83 " pdb=" CG ARGA5 83 " pdb=" CD ARGA5 83 " pdb=" NE ARGA5 83 " ideal model delta sinusoidal sigma weight residual 60.00 119.75 -59.75 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB ARG Q 83 " pdb=" CG ARG Q 83 " pdb=" CD ARG Q 83 " pdb=" NE ARG Q 83 " ideal model delta sinusoidal sigma weight residual 60.00 118.49 -58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB ARG 8 83 " pdb=" CG ARG 8 83 " pdb=" CD ARG 8 83 " pdb=" NE ARG 8 83 " ideal model delta sinusoidal sigma weight residual 60.00 117.87 -57.87 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 24630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 6067 0.070 - 0.139: 350 0.139 - 0.209: 0 0.209 - 0.278: 69 0.278 - 0.348: 69 Chirality restraints: 6555 Sorted by residual: chirality pdb=" C5 LHG 1 201 " pdb=" C4 LHG 1 201 " pdb=" C6 LHG 1 201 " pdb=" O7 LHG 1 201 " both_signs ideal model delta sigma weight residual False -2.53 -2.88 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C5 LHG 8 202 " pdb=" C4 LHG 8 202 " pdb=" C6 LHG 8 202 " pdb=" O7 LHG 8 202 " both_signs ideal model delta sigma weight residual False -2.53 -2.88 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C5 LHG d 201 " pdb=" C4 LHG d 201 " pdb=" C6 LHG d 201 " pdb=" O7 LHG d 201 " both_signs ideal model delta sigma weight residual False -2.53 -2.88 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 6552 not shown) Planarity restraints: 6072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL b 65 " -0.015 5.00e-02 4.00e+02 2.24e-02 8.03e-01 pdb=" N PRO b 66 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO b 66 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO b 66 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL u 65 " -0.015 5.00e-02 4.00e+02 2.20e-02 7.75e-01 pdb=" N PRO u 66 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO u 66 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO u 66 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 7 65 " 0.014 5.00e-02 4.00e+02 2.16e-02 7.47e-01 pdb=" N PRO 7 66 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO 7 66 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO 7 66 " 0.012 5.00e-02 4.00e+02 ... (remaining 6069 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 15735 2.94 - 3.43: 42280 3.43 - 3.92: 66672 3.92 - 4.41: 71202 4.41 - 4.90: 122619 Nonbonded interactions: 318508 Sorted by model distance: nonbonded pdb=" NZ LYS U 87 " pdb=" O1 LHG j 202 " model vdw 2.446 3.120 nonbonded pdb=" OE2 GLU h 48 " pdb=" NH2 ARG h 51 " model vdw 2.493 3.120 nonbonded pdb=" OE2 GLU f 48 " pdb=" NH2 ARG f 51 " model vdw 2.526 3.120 nonbonded pdb=" O1 LHG h 201 " pdb=" O2 LHG h 201 " model vdw 2.532 2.432 nonbonded pdb=" N GLN p 105 " pdb=" OE1 GLN p 105 " model vdw 2.533 3.120 ... (remaining 318503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 44 through 112) selection = (chain '1' and resid 44 through 112) selection = (chain '2' and resid 44 through 112) selection = (chain '3' and resid 44 through 112) selection = (chain '4' and resid 44 through 112) selection = (chain '5' and resid 44 through 112) selection = (chain '6' and resid 44 through 112) selection = chain '7' selection = (chain '8' and resid 44 through 112) selection = (chain '9' and resid 44 through 112) selection = (chain 'A' and resid 44 through 112) selection = (chain 'A1' and resid 44 through 112) selection = (chain 'A2' and resid 44 through 112) selection = (chain 'A3' and resid 44 through 112) selection = (chain 'A4' and resid 44 through 112) selection = (chain 'A5' and resid 44 through 112) selection = (chain 'A6' and resid 44 through 112) selection = chain 'A7' selection = (chain 'B' and resid 44 through 112) selection = chain 'C' selection = (chain 'D' and resid 44 through 112) selection = (chain 'E' and resid 44 through 112) selection = (chain 'F' and resid 44 through 112) selection = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 44 through 112) selection = (chain 'J' and resid 44 through 112) selection = (chain 'K' and resid 44 through 112) selection = (chain 'L' and resid 44 through 112) selection = (chain 'M' and resid 44 through 112) selection = chain 'N' selection = (chain 'O' and resid 44 through 112) selection = (chain 'P' and resid 44 through 112) selection = (chain 'Q' and resid 44 through 112) selection = (chain 'R' and resid 44 through 112) selection = (chain 'S' and resid 44 through 112) selection = chain 'T' selection = (chain 'U' and resid 44 through 112) selection = (chain 'V' and resid 44 through 112) selection = (chain 'W' and resid 44 through 112) selection = (chain 'X' and resid 44 through 112) selection = (chain 'Y' and resid 44 through 112) selection = (chain 'Z' and resid 44 through 112) selection = chain 'a' selection = chain 'b' selection = (chain 'c' and resid 44 through 112) selection = (chain 'd' and resid 44 through 112) selection = chain 'e' selection = (chain 'f' and resid 44 through 112) selection = chain 'g' selection = (chain 'h' and resid 44 through 112) selection = (chain 'i' and resid 44 through 112) selection = (chain 'j' and resid 44 through 112) selection = (chain 'k' and resid 44 through 112) selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = (chain 'p' and resid 44 through 112) selection = (chain 'q' and resid 44 through 112) selection = (chain 'r' and resid 44 through 112) selection = (chain 's' and resid 44 through 112) selection = (chain 't' and resid 44 through 112) selection = (chain 'u' and resid 44 through 112) selection = (chain 'v' and resid 44 through 112) selection = chain 'w' selection = (chain 'x' and resid 44 through 112) selection = chain 'y' selection = (chain 'z' and resid 44 through 112) } 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: 6.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.040 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.060 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 0.015 0.124 39537 Z= 0.749 Angle : 0.886 8.764 52923 Z= 0.361 Chirality : 0.054 0.348 6555 Planarity : 0.002 0.022 6072 Dihedral : 16.805 88.533 15801 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.24 % Allowed : 3.95 % Favored : 91.81 % 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 aren not related in a simple way. whole: 4.46 (0.12), residues: 4623 helix: 3.52 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.45 (0.21), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG n 92 TYR 0.007 0.001 TYR 0 80 PHE 0.005 0.001 PHE P 90 TRP 0.003 0.001 TRP B 93 Details of bonding type rmsd covalent geometry : bond 0.01506 (39537) covalent geometry : angle 0.88632 (52923) hydrogen bonds : bond 0.10549 ( 3134) hydrogen bonds : angle 3.35951 ( 9402) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 858 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7436 (ttm-80) REVERT: F 63 THR cc_start: 0.8445 (m) cc_final: 0.8154 (p) REVERT: F 87 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7006 (tptt) REVERT: G 87 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.6989 (tptt) REVERT: G 92 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7515 (ttm-80) REVERT: H 63 THR cc_start: 0.8536 (m) cc_final: 0.8098 (p) REVERT: I 87 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7159 (tptt) REVERT: I 109 MET cc_start: 0.8849 (ttp) cc_final: 0.8626 (ttm) REVERT: J 86 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7617 (tt0) REVERT: J 87 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7145 (tptt) REVERT: K 83 ARG cc_start: 0.8678 (mtp-110) cc_final: 0.8402 (mtp-110) REVERT: K 87 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7608 (tptt) REVERT: L 60 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: M 63 THR cc_start: 0.8539 (m) cc_final: 0.8235 (p) REVERT: M 83 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.8348 (mtm180) REVERT: 3 51 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7178 (mtt-85) REVERT: 4 49 LYS cc_start: 0.8858 (tttt) cc_final: 0.8497 (ttpt) REVERT: 4 52 SER cc_start: 0.9107 (t) cc_final: 0.8751 (p) REVERT: 4 63 THR cc_start: 0.8411 (m) cc_final: 0.8090 (p) REVERT: 4 109 MET cc_start: 0.8897 (ttp) cc_final: 0.8689 (ttp) REVERT: 5 52 SER cc_start: 0.9140 (t) cc_final: 0.8779 (p) REVERT: 5 87 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7110 (tptt) REVERT: 6 63 THR cc_start: 0.8356 (m) cc_final: 0.8079 (p) REVERT: 6 87 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7277 (tptt) REVERT: 6 99 ILE cc_start: 0.8899 (mt) cc_final: 0.8552 (mp) REVERT: 7 63 THR cc_start: 0.8461 (m) cc_final: 0.8232 (p) REVERT: 7 87 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8107 (pttp) REVERT: 7 99 ILE cc_start: 0.8746 (mt) cc_final: 0.8482 (mt) REVERT: 8 87 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7305 (tptt) REVERT: 9 87 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7331 (tptt) REVERT: A7 87 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7966 (ptmt) REVERT: 0 48 GLU cc_start: 0.7386 (tm-30) cc_final: 0.6954 (tp30) REVERT: 0 87 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7587 (ptmt) REVERT: p 87 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7283 (tptt) REVERT: p 92 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.5837 (tpt170) REVERT: q 87 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7536 (tptt) REVERT: r 63 THR cc_start: 0.8733 (m) cc_final: 0.8497 (p) REVERT: r 87 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.7734 (tptt) REVERT: s 87 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.7630 (tptt) REVERT: t 48 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6963 (tp30) REVERT: t 87 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7269 (tptt) REVERT: u 87 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7404 (tptt) REVERT: v 94 SER cc_start: 0.8736 (m) cc_final: 0.8359 (p) REVERT: x 83 ARG cc_start: 0.8599 (mtp-110) cc_final: 0.8323 (mtp-110) REVERT: z 87 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7641 (tptt) REVERT: c 63 THR cc_start: 0.8732 (m) cc_final: 0.8453 (p) REVERT: c 86 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7704 (tp30) REVERT: c 87 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7025 (tptt) REVERT: f 87 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7298 (tptt) REVERT: g 63 THR cc_start: 0.8276 (m) cc_final: 0.7987 (p) REVERT: g 87 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7813 (tptt) REVERT: h 63 THR cc_start: 0.8577 (m) cc_final: 0.8298 (p) REVERT: h 87 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8363 (ptmt) REVERT: j 87 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7659 (tptt) REVERT: k 87 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7543 (tptt) REVERT: l 87 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7624 (tptt) REVERT: n 87 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8623 (pttt) REVERT: o 83 ARG cc_start: 0.8579 (mtp-110) cc_final: 0.6855 (mmp80) REVERT: O 87 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7278 (tmtt) REVERT: O 94 SER cc_start: 0.8839 (m) cc_final: 0.8539 (p) REVERT: P 52 SER cc_start: 0.9039 (t) cc_final: 0.8704 (p) REVERT: P 87 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7116 (tptt) REVERT: Q 63 THR cc_start: 0.8441 (m) cc_final: 0.8216 (p) REVERT: Q 78 ILE cc_start: 0.8394 (mm) cc_final: 0.8141 (mm) REVERT: Q 87 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7182 (tptt) REVERT: Q 109 MET cc_start: 0.8671 (ttp) cc_final: 0.8464 (ttp) REVERT: R 87 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8170 (pttm) REVERT: S 63 THR cc_start: 0.8193 (m) cc_final: 0.7742 (p) REVERT: U 87 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7376 (tptp) REVERT: W 87 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7190 (tptt) REVERT: W 94 SER cc_start: 0.8657 (m) cc_final: 0.8374 (p) REVERT: X 52 SER cc_start: 0.8246 (t) cc_final: 0.7893 (m) REVERT: X 87 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7373 (tptt) REVERT: Y 87 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7412 (tptt) REVERT: Z 63 THR cc_start: 0.8561 (m) cc_final: 0.8247 (p) REVERT: Z 87 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7149 (tptt) REVERT: a 87 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7863 (ptmt) outliers start: 158 outliers final: 18 residues processed: 898 average time/residue: 0.2303 time to fit residues: 332.9082 Evaluate side-chains 639 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 583 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 60 GLU Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 87 LYS Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain A4 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A7 residue 87 LYS Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 1 residue 87 LYS Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 64 ILE Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain y residue 65 VAL Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 87 LYS Chi-restraints excluded: chain n residue 65 VAL Chi-restraints excluded: chain n residue 87 LYS Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 87 LYS Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN G 59 GLN 1 45 GLN u 45 GLN d 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.092552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.074757 restraints weight = 57419.328| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.91 r_work: 0.2697 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39537 Z= 0.111 Angle : 0.450 8.174 52923 Z= 0.232 Chirality : 0.036 0.122 6555 Planarity : 0.003 0.024 6072 Dihedral : 18.522 89.961 8256 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 4.27 % Allowed : 7.89 % Favored : 87.84 % 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 aren not related in a simple way. whole: 4.51 (0.12), residues: 4623 helix: 3.55 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.40 (0.21), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 51 TYR 0.005 0.001 TYR D 80 PHE 0.005 0.001 PHE A 111 TRP 0.004 0.001 TRPA1 93 Details of bonding type rmsd covalent geometry : bond 0.00242 (39537) covalent geometry : angle 0.44996 (52923) hydrogen bonds : bond 0.03584 ( 3134) hydrogen bonds : angle 3.07503 ( 9402) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 686 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8101 (tp30) cc_final: 0.7667 (tp30) REVERT: E 63 THR cc_start: 0.9148 (p) cc_final: 0.8940 (p) REVERT: F 63 THR cc_start: 0.9019 (m) cc_final: 0.8751 (p) REVERT: F 87 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7538 (tptt) REVERT: G 87 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.7500 (tptt) REVERT: H 63 THR cc_start: 0.9024 (m) cc_final: 0.8820 (p) REVERT: I 87 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.7679 (tptt) REVERT: I 109 MET cc_start: 0.9286 (ttp) cc_final: 0.9068 (ttm) REVERT: J 86 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8058 (tt0) REVERT: J 87 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.7716 (tptt) REVERT: K 83 ARG cc_start: 0.9059 (mtp-110) cc_final: 0.8799 (mtp-110) REVERT: K 87 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8094 (tptt) REVERT: M 63 THR cc_start: 0.8956 (m) cc_final: 0.8711 (p) REVERT: M 83 ARG cc_start: 0.9178 (mtp-110) cc_final: 0.8840 (mtm180) REVERT: 3 51 ARG cc_start: 0.8622 (ttp80) cc_final: 0.7230 (mtt-85) REVERT: 4 49 LYS cc_start: 0.8875 (tttt) cc_final: 0.8625 (ttpt) REVERT: 4 52 SER cc_start: 0.9217 (t) cc_final: 0.8852 (p) REVERT: 5 52 SER cc_start: 0.9371 (t) cc_final: 0.9054 (p) REVERT: 5 73 LEU cc_start: 0.9425 (tp) cc_final: 0.9125 (tp) REVERT: 5 87 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.7434 (tptt) REVERT: 6 63 THR cc_start: 0.8823 (m) cc_final: 0.8563 (p) REVERT: 6 87 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7435 (tptt) REVERT: 8 87 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7778 (tptt) REVERT: 9 87 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.7711 (tptt) REVERT: A6 86 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8253 (pm20) REVERT: 0 48 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7998 (tp30) REVERT: 0 87 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8163 (ptmt) REVERT: 1 86 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8525 (mm-30) REVERT: p 87 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.7401 (tptt) REVERT: p 92 ARG cc_start: 0.8840 (ttm-80) cc_final: 0.6095 (tpt170) REVERT: q 87 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.7700 (tptt) REVERT: r 87 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.7932 (tptt) REVERT: s 87 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.7777 (tptt) REVERT: t 48 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8058 (tp30) REVERT: t 87 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.7668 (tptt) REVERT: u 45 GLN cc_start: 0.8540 (mt0) cc_final: 0.8320 (mt0) REVERT: u 87 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.7565 (tptt) REVERT: v 94 SER cc_start: 0.9363 (m) cc_final: 0.9136 (p) REVERT: x 99 ILE cc_start: 0.9464 (mt) cc_final: 0.9131 (mp) REVERT: z 87 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.7904 (tptt) REVERT: c 63 THR cc_start: 0.8950 (m) cc_final: 0.8724 (p) REVERT: c 87 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.7336 (tptt) REVERT: f 87 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.7796 (tptt) REVERT: g 63 THR cc_start: 0.8759 (m) cc_final: 0.8499 (p) REVERT: g 87 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8075 (tptt) REVERT: h 87 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8723 (ptmt) REVERT: j 87 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8017 (tptt) REVERT: k 87 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.7986 (tptt) REVERT: l 87 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.7946 (tptt) REVERT: o 83 ARG cc_start: 0.8895 (mtp-110) cc_final: 0.7340 (mmp80) REVERT: O 87 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.7683 (tptt) REVERT: P 48 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8046 (tp30) REVERT: P 52 SER cc_start: 0.9169 (t) cc_final: 0.8739 (p) REVERT: P 87 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7538 (tptt) REVERT: Q 78 ILE cc_start: 0.9172 (mm) cc_final: 0.8970 (mm) REVERT: Q 87 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7574 (tptt) REVERT: S 63 THR cc_start: 0.8825 (m) cc_final: 0.8504 (p) REVERT: U 87 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.7805 (tptt) REVERT: W 87 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.7496 (tptt) REVERT: X 52 SER cc_start: 0.8910 (t) cc_final: 0.8581 (m) REVERT: X 87 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.7786 (tptt) REVERT: Y 87 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.7795 (tptt) REVERT: Z 63 THR cc_start: 0.9052 (m) cc_final: 0.8772 (p) REVERT: Z 87 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7569 (tptt) REVERT: Z 89 THR cc_start: 0.9289 (t) cc_final: 0.9042 (p) REVERT: a 63 THR cc_start: 0.9144 (m) cc_final: 0.8936 (p) REVERT: a 87 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8593 (ptmt) REVERT: b 86 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8583 (mm-30) outliers start: 159 outliers final: 65 residues processed: 783 average time/residue: 0.2392 time to fit residues: 308.8007 Evaluate side-chains 671 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 573 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 65 VAL Chi-restraints excluded: chain 5 residue 64 ILE Chi-restraints excluded: chain 5 residue 78 ILE Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 65 VAL Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 64 ILE Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain A1 residue 65 VAL Chi-restraints excluded: chain A2 residue 65 VAL Chi-restraints excluded: chain A3 residue 65 VAL Chi-restraints excluded: chain A4 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A6 residue 65 VAL Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 2 residue 65 VAL Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 64 ILE Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 87 LYS Chi-restraints excluded: chain n residue 65 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 385 optimal weight: 0.9990 chunk 365 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 291 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 177 optimal weight: 4.9990 chunk 382 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 = 0.3094 r_free = 0.3094 target = 0.091435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.074107 restraints weight = 57965.321| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.91 r_work: 0.2664 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 39537 Z= 0.145 Angle : 0.460 10.524 52923 Z= 0.233 Chirality : 0.037 0.159 6555 Planarity : 0.003 0.023 6072 Dihedral : 17.883 89.847 8229 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.46 % Allowed : 8.91 % Favored : 86.63 % 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 aren not related in a simple way. whole: 4.47 (0.12), residues: 4623 helix: 3.53 (0.08), residues: 4209 sheet: None (None), residues: 0 loop : -4.41 (0.21), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 51 TYR 0.007 0.001 TYR 0 80 PHE 0.007 0.001 PHE O 111 TRP 0.003 0.001 TRP a 93 Details of bonding type rmsd covalent geometry : bond 0.00358 (39537) covalent geometry : angle 0.45980 (52923) hydrogen bonds : bond 0.03820 ( 3134) hydrogen bonds : angle 3.03182 ( 9402) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 607 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8168 (tp30) cc_final: 0.7740 (tp30) REVERT: F 63 THR cc_start: 0.9055 (m) cc_final: 0.8779 (p) REVERT: F 87 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.7541 (tptt) REVERT: G 87 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.7524 (tptt) REVERT: H 63 THR cc_start: 0.9095 (m) cc_final: 0.8678 (p) REVERT: I 87 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.7704 (tptt) REVERT: I 109 MET cc_start: 0.9303 (ttp) cc_final: 0.9088 (ttm) REVERT: J 86 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8052 (tt0) REVERT: J 87 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.7691 (tptt) REVERT: K 83 ARG cc_start: 0.9087 (mtp-110) cc_final: 0.8786 (mtp-110) REVERT: K 87 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8112 (tptt) REVERT: L 60 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8795 (mm-30) REVERT: M 63 THR cc_start: 0.9007 (m) cc_final: 0.8722 (p) REVERT: M 83 ARG cc_start: 0.9145 (mtp-110) cc_final: 0.8793 (mtm180) REVERT: 3 51 ARG cc_start: 0.8646 (ttp80) cc_final: 0.7287 (mtt-85) REVERT: 4 49 LYS cc_start: 0.8869 (tttt) cc_final: 0.8603 (ttpt) REVERT: 4 51 ARG cc_start: 0.8472 (ttm-80) cc_final: 0.8160 (ttm-80) REVERT: 4 52 SER cc_start: 0.9279 (t) cc_final: 0.8878 (p) REVERT: 5 52 SER cc_start: 0.9370 (t) cc_final: 0.9015 (p) REVERT: 5 73 LEU cc_start: 0.9451 (tp) cc_final: 0.9124 (tp) REVERT: 5 87 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.7370 (tptt) REVERT: 6 63 THR cc_start: 0.8858 (m) cc_final: 0.8579 (p) REVERT: 6 87 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7516 (tptt) REVERT: 8 87 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.7844 (tptt) REVERT: 9 87 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.7833 (tptt) REVERT: A6 86 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8311 (pm20) REVERT: 0 48 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8100 (tp30) REVERT: 0 83 ARG cc_start: 0.9290 (mtp85) cc_final: 0.9059 (mtp85) REVERT: 0 87 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8164 (ptmt) REVERT: p 87 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7430 (tptt) REVERT: q 87 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.7772 (tptt) REVERT: r 87 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8004 (tptt) REVERT: s 87 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.7815 (tptt) REVERT: t 48 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8124 (tp30) REVERT: t 87 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.7674 (tptt) REVERT: t 88 ASP cc_start: 0.9081 (p0) cc_final: 0.8735 (p0) REVERT: u 87 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.7595 (tptt) REVERT: v 94 SER cc_start: 0.9405 (m) cc_final: 0.9156 (p) REVERT: x 99 ILE cc_start: 0.9463 (mt) cc_final: 0.9134 (mp) REVERT: y 87 LYS cc_start: 0.8476 (ptmt) cc_final: 0.8198 (ptmt) REVERT: z 87 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.7906 (tptt) REVERT: c 63 THR cc_start: 0.8976 (m) cc_final: 0.8739 (p) REVERT: c 87 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.7278 (tptt) REVERT: f 87 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.7794 (tptt) REVERT: g 63 THR cc_start: 0.8755 (m) cc_final: 0.8487 (p) REVERT: g 87 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.7867 (tptt) REVERT: h 87 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8761 (ptmt) REVERT: i 88 ASP cc_start: 0.9186 (p0) cc_final: 0.8947 (p0) REVERT: j 87 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8034 (tptt) REVERT: k 87 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8013 (tptt) REVERT: l 87 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.7951 (tptt) REVERT: O 87 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7715 (tptt) REVERT: P 87 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7589 (tptt) REVERT: Q 87 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.7627 (tptt) REVERT: S 63 THR cc_start: 0.8903 (m) cc_final: 0.8626 (p) REVERT: U 87 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.7810 (tptt) REVERT: W 87 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.7473 (tptt) REVERT: X 52 SER cc_start: 0.8978 (t) cc_final: 0.8643 (m) REVERT: X 87 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.7796 (tptt) REVERT: Y 87 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.7845 (tptt) REVERT: Z 63 THR cc_start: 0.9108 (m) cc_final: 0.8817 (p) REVERT: Z 87 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.7674 (tptt) REVERT: a 63 THR cc_start: 0.9149 (m) cc_final: 0.8946 (p) REVERT: a 87 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8549 (ptmt) REVERT: b 86 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8579 (mm-30) outliers start: 166 outliers final: 85 residues processed: 718 average time/residue: 0.2416 time to fit residues: 284.6415 Evaluate side-chains 681 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 563 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 65 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 65 VAL Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 64 ILE Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain A1 residue 64 ILE Chi-restraints excluded: chain A1 residue 65 VAL Chi-restraints excluded: chain A2 residue 65 VAL Chi-restraints excluded: chain A2 residue 99 ILE Chi-restraints excluded: chain A3 residue 65 VAL Chi-restraints excluded: chain A4 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A6 residue 65 VAL Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 2 residue 65 VAL Chi-restraints excluded: chain p residue 52 SER Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 54 LEU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain u residue 62 THR Chi-restraints excluded: chain u residue 63 THR Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain w residue 86 GLU Chi-restraints excluded: chain x residue 64 ILE Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 65 VAL Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain n residue 65 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 52 SER Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain W residue 52 SER Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 94 SER Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 245 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 312 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 105 GLN u 45 GLN y 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.092151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.074498 restraints weight = 57606.036| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.91 r_work: 0.2688 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39537 Z= 0.109 Angle : 0.419 7.709 52923 Z= 0.219 Chirality : 0.036 0.132 6555 Planarity : 0.003 0.025 6072 Dihedral : 17.459 88.365 8222 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.80 % Allowed : 9.18 % Favored : 86.02 % 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 aren not related in a simple way. whole: 4.74 (0.12), residues: 4623 helix: 3.71 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.46 (0.20), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 51 TYR 0.005 0.001 TYR q 80 PHE 0.005 0.000 PHE A 111 TRP 0.004 0.001 TRP F 93 Details of bonding type rmsd covalent geometry : bond 0.00248 (39537) covalent geometry : angle 0.41940 (52923) hydrogen bonds : bond 0.03283 ( 3134) hydrogen bonds : angle 2.87619 ( 9402) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 650 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8185 (tp30) cc_final: 0.7761 (tp30) REVERT: B 60 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8662 (mm-30) REVERT: F 63 THR cc_start: 0.9031 (m) cc_final: 0.8761 (p) REVERT: F 87 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.7516 (tptt) REVERT: G 87 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.7543 (tptt) REVERT: H 63 THR cc_start: 0.9056 (m) cc_final: 0.8817 (p) REVERT: I 87 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.7680 (tptt) REVERT: I 109 MET cc_start: 0.9284 (ttp) cc_final: 0.9080 (ttm) REVERT: J 86 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8146 (tt0) REVERT: J 87 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.7709 (tptt) REVERT: K 83 ARG cc_start: 0.9078 (mtp-110) cc_final: 0.8743 (mtp-110) REVERT: K 86 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7917 (pm20) REVERT: K 87 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8135 (tptt) REVERT: M 63 THR cc_start: 0.8963 (m) cc_final: 0.8690 (p) REVERT: M 83 ARG cc_start: 0.9148 (mtp-110) cc_final: 0.8804 (mtm180) REVERT: 3 51 ARG cc_start: 0.8656 (ttp80) cc_final: 0.7226 (mtt-85) REVERT: 4 49 LYS cc_start: 0.8845 (tttt) cc_final: 0.8580 (ttpt) REVERT: 4 51 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8119 (ttm-80) REVERT: 4 52 SER cc_start: 0.9271 (t) cc_final: 0.8884 (p) REVERT: 5 52 SER cc_start: 0.9353 (t) cc_final: 0.9047 (p) REVERT: 5 73 LEU cc_start: 0.9391 (tp) cc_final: 0.9109 (tp) REVERT: 5 87 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.7458 (tptt) REVERT: 6 63 THR cc_start: 0.8841 (m) cc_final: 0.8574 (p) REVERT: 6 87 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.7548 (tptt) REVERT: 8 87 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7837 (tptt) REVERT: 9 87 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.7855 (tptt) REVERT: A5 102 SER cc_start: 0.9112 (p) cc_final: 0.8899 (t) REVERT: A6 86 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8339 (pm20) REVERT: 0 48 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8174 (tp30) REVERT: 0 83 ARG cc_start: 0.9217 (mtp85) cc_final: 0.8952 (mtp85) REVERT: 0 87 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8167 (ptmt) REVERT: 2 48 GLU cc_start: 0.8486 (tp30) cc_final: 0.8251 (tp30) REVERT: p 87 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7340 (tptt) REVERT: q 87 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.7752 (tptt) REVERT: r 87 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8045 (tptt) REVERT: s 87 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.7807 (tptt) REVERT: t 48 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8141 (tp30) REVERT: t 87 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.7696 (tptt) REVERT: u 87 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.7581 (tptt) REVERT: v 94 SER cc_start: 0.9388 (m) cc_final: 0.9151 (p) REVERT: x 99 ILE cc_start: 0.9428 (mt) cc_final: 0.9205 (mt) REVERT: y 45 GLN cc_start: 0.7974 (mt0) cc_final: 0.7756 (pt0) REVERT: z 87 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.7931 (tptt) REVERT: c 63 THR cc_start: 0.8955 (m) cc_final: 0.8726 (p) REVERT: c 87 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.7339 (tptt) REVERT: f 87 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.7810 (tptt) REVERT: g 63 THR cc_start: 0.8740 (m) cc_final: 0.8478 (p) REVERT: g 87 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8055 (tptt) REVERT: h 87 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8802 (ptmt) REVERT: i 88 ASP cc_start: 0.9212 (p0) cc_final: 0.8948 (p0) REVERT: j 87 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8030 (tptt) REVERT: k 87 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8017 (tptt) REVERT: l 87 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.7950 (tptt) REVERT: o 89 THR cc_start: 0.9197 (t) cc_final: 0.8879 (p) REVERT: O 87 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7680 (tptt) REVERT: P 52 SER cc_start: 0.9144 (t) cc_final: 0.8767 (p) REVERT: P 87 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7559 (tptt) REVERT: Q 87 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.7607 (tptt) REVERT: S 63 THR cc_start: 0.8815 (m) cc_final: 0.8519 (p) REVERT: T 63 THR cc_start: 0.9131 (m) cc_final: 0.8826 (p) REVERT: U 87 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.7795 (tptt) REVERT: W 83 ARG cc_start: 0.9347 (mtp85) cc_final: 0.9082 (mtp85) REVERT: W 87 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.7543 (tptt) REVERT: X 52 SER cc_start: 0.8924 (t) cc_final: 0.8603 (m) REVERT: X 87 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.7788 (tptt) REVERT: Y 87 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7865 (tptt) REVERT: Z 63 THR cc_start: 0.9079 (m) cc_final: 0.8771 (p) REVERT: Z 87 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.7652 (tptt) REVERT: a 63 THR cc_start: 0.9151 (m) cc_final: 0.8941 (p) REVERT: a 87 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8603 (ptmt) REVERT: b 86 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8565 (mm-30) outliers start: 179 outliers final: 87 residues processed: 768 average time/residue: 0.2186 time to fit residues: 277.4743 Evaluate side-chains 703 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 583 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 4 residue 65 VAL Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 65 VAL Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 64 ILE Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain A1 residue 64 ILE Chi-restraints excluded: chain A1 residue 65 VAL Chi-restraints excluded: chain A1 residue 85 ILE Chi-restraints excluded: chain A2 residue 64 ILE Chi-restraints excluded: chain A2 residue 65 VAL Chi-restraints excluded: chain A2 residue 99 ILE Chi-restraints excluded: chain A3 residue 65 VAL Chi-restraints excluded: chain A4 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A6 residue 65 VAL Chi-restraints excluded: chain A7 residue 64 ILE Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 2 residue 65 VAL Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 64 ILE Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 65 VAL Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain f residue 62 THR Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 52 SER Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 52 SER Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 279 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 379 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 388 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 122 optimal weight: 0.0970 chunk 293 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3114 r_free = 0.3114 target = 0.092195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.074561 restraints weight = 57541.046| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 1.93 r_work: 0.2683 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39537 Z= 0.113 Angle : 0.423 9.622 52923 Z= 0.220 Chirality : 0.036 0.166 6555 Planarity : 0.003 0.024 6072 Dihedral : 17.123 88.332 8221 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.46 % Allowed : 10.39 % Favored : 85.16 % 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 aren not related in a simple way. whole: 4.84 (0.12), residues: 4623 helix: 3.78 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.45 (0.20), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 51 TYR 0.005 0.001 TYR D 80 PHE 0.005 0.001 PHE A 111 TRP 0.004 0.001 TRP 3 93 Details of bonding type rmsd covalent geometry : bond 0.00265 (39537) covalent geometry : angle 0.42345 (52923) hydrogen bonds : bond 0.03284 ( 3134) hydrogen bonds : angle 2.84145 ( 9402) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 617 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8226 (tp30) cc_final: 0.7805 (tp30) REVERT: B 60 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8710 (mm-30) REVERT: F 63 THR cc_start: 0.9033 (m) cc_final: 0.8759 (p) REVERT: F 87 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.7594 (tptt) REVERT: G 87 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.7618 (tptt) REVERT: H 63 THR cc_start: 0.9072 (m) cc_final: 0.8814 (p) REVERT: I 87 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.7692 (tptt) REVERT: I 109 MET cc_start: 0.9308 (ttp) cc_final: 0.9094 (ttm) REVERT: J 86 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8074 (tt0) REVERT: J 87 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7740 (tptt) REVERT: K 83 ARG cc_start: 0.9069 (mtp-110) cc_final: 0.8730 (mtp-110) REVERT: K 86 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7941 (pm20) REVERT: K 87 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8140 (tptt) REVERT: M 63 THR cc_start: 0.8974 (m) cc_final: 0.8708 (p) REVERT: M 83 ARG cc_start: 0.9144 (mtp-110) cc_final: 0.8745 (mtm180) REVERT: 3 51 ARG cc_start: 0.8669 (ttp80) cc_final: 0.7231 (mtt-85) REVERT: 4 48 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7801 (tp30) REVERT: 4 49 LYS cc_start: 0.8835 (tttt) cc_final: 0.8582 (ttpt) REVERT: 4 51 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.8059 (ttm-80) REVERT: 4 52 SER cc_start: 0.9258 (t) cc_final: 0.8818 (p) REVERT: 5 52 SER cc_start: 0.9335 (t) cc_final: 0.9018 (p) REVERT: 5 73 LEU cc_start: 0.9396 (tp) cc_final: 0.9127 (tp) REVERT: 5 87 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.7493 (tptt) REVERT: 6 63 THR cc_start: 0.8846 (m) cc_final: 0.8584 (p) REVERT: 6 87 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7549 (tptt) REVERT: 8 87 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.7900 (tptt) REVERT: 9 87 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.7857 (tptt) REVERT: A6 86 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8322 (pm20) REVERT: 0 48 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8194 (tp30) REVERT: 0 87 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8201 (ptmt) REVERT: 2 48 GLU cc_start: 0.8436 (tp30) cc_final: 0.8190 (tp30) REVERT: p 87 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.7342 (tptt) REVERT: q 87 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.7753 (tptt) REVERT: r 87 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8043 (tptt) REVERT: s 87 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.7805 (tptt) REVERT: t 48 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8151 (tp30) REVERT: t 87 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.7727 (tptt) REVERT: u 87 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.7567 (tptt) REVERT: v 94 SER cc_start: 0.9383 (m) cc_final: 0.9157 (p) REVERT: x 99 ILE cc_start: 0.9427 (mt) cc_final: 0.9193 (mt) REVERT: y 45 GLN cc_start: 0.8005 (mt0) cc_final: 0.7759 (pt0) REVERT: z 87 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.7911 (tptt) REVERT: c 63 THR cc_start: 0.8951 (m) cc_final: 0.8726 (p) REVERT: c 87 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.7340 (tptt) REVERT: d 48 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7422 (mt-10) REVERT: f 87 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.7819 (tptt) REVERT: g 63 THR cc_start: 0.8764 (m) cc_final: 0.8522 (p) REVERT: g 87 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8051 (tptt) REVERT: h 87 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8799 (ptmt) REVERT: i 88 ASP cc_start: 0.9197 (p0) cc_final: 0.8921 (p0) REVERT: j 87 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8027 (tptt) REVERT: k 87 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8024 (tptt) REVERT: l 87 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.7972 (tptt) REVERT: o 89 THR cc_start: 0.9214 (t) cc_final: 0.8896 (p) REVERT: O 87 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.7686 (tptt) REVERT: P 52 SER cc_start: 0.9171 (t) cc_final: 0.8786 (p) REVERT: P 87 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7562 (tptt) REVERT: Q 87 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7661 (tptt) REVERT: S 51 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8202 (ttm-80) REVERT: S 63 THR cc_start: 0.8899 (m) cc_final: 0.8636 (p) REVERT: T 63 THR cc_start: 0.9120 (m) cc_final: 0.8829 (p) REVERT: U 87 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.7803 (tptt) REVERT: W 83 ARG cc_start: 0.9361 (mtp85) cc_final: 0.9087 (mtp85) REVERT: W 87 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.7574 (tptt) REVERT: X 52 SER cc_start: 0.8943 (t) cc_final: 0.8618 (m) REVERT: X 87 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.7816 (tptt) REVERT: Y 51 ARG cc_start: 0.8327 (ttp80) cc_final: 0.8107 (ttm110) REVERT: Y 87 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.7885 (tptt) REVERT: Z 63 THR cc_start: 0.9087 (m) cc_final: 0.8789 (p) REVERT: Z 87 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7656 (tptt) REVERT: a 63 THR cc_start: 0.9157 (m) cc_final: 0.8950 (p) REVERT: a 87 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8609 (ptmt) REVERT: b 86 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8548 (mm-30) outliers start: 166 outliers final: 93 residues processed: 726 average time/residue: 0.2583 time to fit residues: 308.8847 Evaluate side-chains 713 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 587 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 4 residue 65 VAL Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 65 VAL Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 64 ILE Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain A1 residue 64 ILE Chi-restraints excluded: chain A1 residue 65 VAL Chi-restraints excluded: chain A1 residue 85 ILE Chi-restraints excluded: chain A2 residue 64 ILE Chi-restraints excluded: chain A2 residue 65 VAL Chi-restraints excluded: chain A2 residue 99 ILE Chi-restraints excluded: chain A3 residue 65 VAL Chi-restraints excluded: chain A4 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A6 residue 65 VAL Chi-restraints excluded: chain A7 residue 64 ILE Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 2 residue 65 VAL Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 64 ILE Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 65 VAL Chi-restraints excluded: chain z residue 64 ILE Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain n residue 65 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 52 SER Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 210 optimal weight: 10.0000 chunk 391 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 379 optimal weight: 3.9990 chunk 295 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 45 GLN p 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.092354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.074706 restraints weight = 57601.764| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.93 r_work: 0.2694 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39537 Z= 0.112 Angle : 0.422 8.416 52923 Z= 0.221 Chirality : 0.036 0.142 6555 Planarity : 0.003 0.035 6072 Dihedral : 16.805 89.026 8221 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.46 % Allowed : 10.57 % Favored : 84.97 % 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 aren not related in a simple way. whole: 4.91 (0.12), residues: 4623 helix: 3.83 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.47 (0.20), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGA3 51 TYR 0.004 0.001 TYR 1 80 PHE 0.005 0.001 PHE 1 90 TRP 0.004 0.001 TRP F 93 Details of bonding type rmsd covalent geometry : bond 0.00264 (39537) covalent geometry : angle 0.42224 (52923) hydrogen bonds : bond 0.03196 ( 3134) hydrogen bonds : angle 2.81105 ( 9402) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 625 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8217 (tp30) cc_final: 0.7792 (tp30) REVERT: B 60 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8751 (mm-30) REVERT: F 63 THR cc_start: 0.9041 (m) cc_final: 0.8768 (p) REVERT: F 83 ARG cc_start: 0.9088 (mtp85) cc_final: 0.8488 (mtp85) REVERT: F 87 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.7598 (tptt) REVERT: G 87 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.7631 (tptt) REVERT: H 63 THR cc_start: 0.9044 (m) cc_final: 0.8783 (p) REVERT: I 87 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.7688 (tptt) REVERT: I 109 MET cc_start: 0.9298 (ttp) cc_final: 0.9091 (ttm) REVERT: J 86 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8138 (tt0) REVERT: J 87 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7686 (tptt) REVERT: K 83 ARG cc_start: 0.9069 (mtp-110) cc_final: 0.8724 (mtp-110) REVERT: K 86 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7947 (pm20) REVERT: K 87 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8146 (tptt) REVERT: L 60 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8755 (mm-30) REVERT: M 45 GLN cc_start: 0.8533 (mt0) cc_final: 0.8250 (mt0) REVERT: M 63 THR cc_start: 0.8966 (m) cc_final: 0.8707 (p) REVERT: M 83 ARG cc_start: 0.9137 (mtp-110) cc_final: 0.8752 (mtm180) REVERT: 3 51 ARG cc_start: 0.8661 (ttp80) cc_final: 0.7207 (mtt-85) REVERT: 3 60 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8800 (mm-30) REVERT: 4 48 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7787 (tp30) REVERT: 4 49 LYS cc_start: 0.8846 (tttt) cc_final: 0.8596 (ttpt) REVERT: 4 51 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.8004 (ttm-80) REVERT: 4 52 SER cc_start: 0.9223 (t) cc_final: 0.8785 (p) REVERT: 5 52 SER cc_start: 0.9337 (t) cc_final: 0.9044 (p) REVERT: 5 73 LEU cc_start: 0.9411 (tp) cc_final: 0.9145 (tp) REVERT: 5 87 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.7467 (tptt) REVERT: 6 63 THR cc_start: 0.8843 (m) cc_final: 0.8590 (p) REVERT: 6 87 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7554 (tptt) REVERT: 8 87 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7911 (tptt) REVERT: 9 87 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.7861 (tptt) REVERT: A6 45 GLN cc_start: 0.8249 (mt0) cc_final: 0.8005 (tt0) REVERT: A6 86 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8338 (pm20) REVERT: 0 48 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8178 (tp30) REVERT: 0 87 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8266 (ptmt) REVERT: p 87 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7314 (tptt) REVERT: q 87 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.7773 (tptt) REVERT: r 87 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8095 (tptt) REVERT: s 87 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.7793 (tptt) REVERT: t 48 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8171 (tp30) REVERT: t 86 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7978 (pm20) REVERT: t 87 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.7759 (tptt) REVERT: t 88 ASP cc_start: 0.9008 (p0) cc_final: 0.8592 (p0) REVERT: u 87 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.7577 (tptt) REVERT: v 94 SER cc_start: 0.9388 (m) cc_final: 0.9163 (p) REVERT: x 99 ILE cc_start: 0.9433 (mt) cc_final: 0.9204 (mt) REVERT: z 87 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.7947 (tptt) REVERT: c 63 THR cc_start: 0.8957 (m) cc_final: 0.8731 (p) REVERT: c 87 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7328 (tptt) REVERT: d 48 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7422 (mt-10) REVERT: d 83 ARG cc_start: 0.9063 (mtp85) cc_final: 0.8761 (mtp85) REVERT: f 87 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.7874 (tptt) REVERT: g 63 THR cc_start: 0.8791 (m) cc_final: 0.8564 (p) REVERT: g 87 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8044 (tptt) REVERT: h 87 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8787 (ptmt) REVERT: i 48 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7427 (mp0) REVERT: i 88 ASP cc_start: 0.9149 (p0) cc_final: 0.8862 (p0) REVERT: j 87 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8013 (tptt) REVERT: k 87 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8029 (tptt) REVERT: l 87 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.7979 (tptt) REVERT: o 63 THR cc_start: 0.8924 (m) cc_final: 0.8706 (p) REVERT: o 83 ARG cc_start: 0.8808 (mtp-110) cc_final: 0.7112 (tpp-160) REVERT: O 51 ARG cc_start: 0.8755 (ttp80) cc_final: 0.7554 (ttm170) REVERT: O 87 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.7661 (tptt) REVERT: P 52 SER cc_start: 0.9169 (t) cc_final: 0.8786 (p) REVERT: P 87 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7544 (tptt) REVERT: Q 87 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.7666 (tptt) REVERT: S 51 ARG cc_start: 0.8604 (ttm-80) cc_final: 0.8218 (ttm-80) REVERT: S 63 THR cc_start: 0.8887 (m) cc_final: 0.8646 (p) REVERT: T 60 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8764 (mm-30) REVERT: T 63 THR cc_start: 0.9064 (m) cc_final: 0.8782 (p) REVERT: U 87 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.7803 (tptt) REVERT: W 83 ARG cc_start: 0.9360 (mtp85) cc_final: 0.9076 (mtp85) REVERT: W 87 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.7577 (tptt) REVERT: X 52 SER cc_start: 0.8910 (t) cc_final: 0.8586 (m) REVERT: X 87 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.7827 (tptt) REVERT: Y 51 ARG cc_start: 0.8305 (ttp80) cc_final: 0.8080 (ttm110) REVERT: Y 87 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.7894 (tptt) REVERT: Z 63 THR cc_start: 0.9056 (m) cc_final: 0.8767 (p) REVERT: Z 87 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7654 (tptt) REVERT: a 63 THR cc_start: 0.9144 (m) cc_final: 0.8941 (p) REVERT: a 87 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8598 (ptmt) outliers start: 166 outliers final: 102 residues processed: 730 average time/residue: 0.2579 time to fit residues: 307.3680 Evaluate side-chains 730 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 595 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 4 residue 65 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 65 VAL Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 64 ILE Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 64 ILE Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain A1 residue 64 ILE Chi-restraints excluded: chain A1 residue 65 VAL Chi-restraints excluded: chain A1 residue 85 ILE Chi-restraints excluded: chain A2 residue 64 ILE Chi-restraints excluded: chain A2 residue 65 VAL Chi-restraints excluded: chain A2 residue 99 ILE Chi-restraints excluded: chain A3 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A6 residue 65 VAL Chi-restraints excluded: chain A7 residue 64 ILE Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 2 residue 65 VAL Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain p residue 105 GLN Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 64 ILE Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain t residue 99 ILE Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 65 VAL Chi-restraints excluded: chain z residue 64 ILE Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain n residue 65 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 52 SER Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 94 SER Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 311 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 278 optimal weight: 0.6980 chunk 381 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 341 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 45 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.091049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.073472 restraints weight = 57943.896| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.93 r_work: 0.2667 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39537 Z= 0.139 Angle : 0.439 7.236 52923 Z= 0.228 Chirality : 0.037 0.147 6555 Planarity : 0.003 0.056 6072 Dihedral : 16.636 86.816 8220 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 4.29 % Allowed : 11.08 % Favored : 84.62 % 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 aren not related in a simple way. whole: 4.81 (0.12), residues: 4623 helix: 3.77 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.46 (0.20), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 0 83 TYR 0.006 0.001 TYR 1 80 PHE 0.007 0.001 PHE r 111 TRP 0.004 0.001 TRP F 93 Details of bonding type rmsd covalent geometry : bond 0.00348 (39537) covalent geometry : angle 0.43920 (52923) hydrogen bonds : bond 0.03412 ( 3134) hydrogen bonds : angle 2.87336 ( 9402) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 598 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8248 (tp30) cc_final: 0.7911 (tp30) REVERT: B 60 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8749 (mm-30) REVERT: F 63 THR cc_start: 0.9057 (m) cc_final: 0.8776 (p) REVERT: F 87 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.7526 (tptt) REVERT: G 87 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.7627 (tptt) REVERT: H 63 THR cc_start: 0.9069 (m) cc_final: 0.8786 (p) REVERT: I 87 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.7706 (tptt) REVERT: I 109 MET cc_start: 0.9307 (ttp) cc_final: 0.9101 (ttm) REVERT: J 86 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8033 (tt0) REVERT: J 87 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.7714 (tptt) REVERT: K 83 ARG cc_start: 0.9026 (mtp-110) cc_final: 0.8718 (mtp-110) REVERT: K 86 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7950 (pm20) REVERT: K 87 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8089 (tptt) REVERT: L 60 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8755 (mm-30) REVERT: M 45 GLN cc_start: 0.8492 (mt0) cc_final: 0.8200 (mt0) REVERT: M 63 THR cc_start: 0.8988 (m) cc_final: 0.8719 (p) REVERT: M 83 ARG cc_start: 0.9131 (mtp-110) cc_final: 0.8737 (mtm180) REVERT: 3 51 ARG cc_start: 0.8687 (ttp80) cc_final: 0.7225 (mtt-85) REVERT: 3 60 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8822 (mm-30) REVERT: 4 48 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7875 (tp30) REVERT: 4 49 LYS cc_start: 0.8871 (tttt) cc_final: 0.8608 (ttpt) REVERT: 4 51 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8006 (ttm-80) REVERT: 4 52 SER cc_start: 0.9235 (t) cc_final: 0.8801 (p) REVERT: 5 52 SER cc_start: 0.9339 (t) cc_final: 0.9040 (p) REVERT: 5 73 LEU cc_start: 0.9406 (tp) cc_final: 0.9137 (tp) REVERT: 5 87 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7478 (tptt) REVERT: 6 63 THR cc_start: 0.8862 (m) cc_final: 0.8588 (p) REVERT: 6 87 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.7534 (tptt) REVERT: 8 87 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.7911 (tptt) REVERT: 9 87 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.7846 (tptt) REVERT: A6 45 GLN cc_start: 0.8328 (mt0) cc_final: 0.7941 (tt0) REVERT: A6 86 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8331 (pm20) REVERT: 0 48 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8221 (tp30) REVERT: 0 87 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8221 (ptmt) REVERT: 2 60 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8839 (mm-30) REVERT: p 87 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7297 (tptt) REVERT: q 87 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.7740 (tptt) REVERT: r 87 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8080 (tptt) REVERT: s 87 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.7832 (tptt) REVERT: t 48 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8186 (tp30) REVERT: t 86 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8034 (pm20) REVERT: t 87 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.7764 (tptt) REVERT: u 87 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.7535 (tptt) REVERT: v 94 SER cc_start: 0.9407 (m) cc_final: 0.9159 (p) REVERT: x 99 ILE cc_start: 0.9446 (mt) cc_final: 0.9212 (mt) REVERT: z 87 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.7942 (tptt) REVERT: c 63 THR cc_start: 0.8958 (m) cc_final: 0.8724 (p) REVERT: c 87 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.7338 (tptt) REVERT: d 48 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7437 (mt-10) REVERT: d 83 ARG cc_start: 0.9075 (mtp85) cc_final: 0.8762 (mtp85) REVERT: f 87 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.7844 (tptt) REVERT: g 63 THR cc_start: 0.8769 (m) cc_final: 0.8535 (p) REVERT: g 87 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8073 (tptt) REVERT: h 87 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8778 (ptmt) REVERT: i 48 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7411 (mp0) REVERT: i 88 ASP cc_start: 0.9129 (p0) cc_final: 0.8829 (p0) REVERT: j 87 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8018 (tptt) REVERT: k 87 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8000 (tptt) REVERT: l 87 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.7972 (tptt) REVERT: O 51 ARG cc_start: 0.8759 (ttp80) cc_final: 0.7544 (ttm170) REVERT: O 87 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7680 (tptt) REVERT: P 52 SER cc_start: 0.9152 (t) cc_final: 0.8764 (p) REVERT: P 87 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7551 (tptt) REVERT: Q 87 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.7664 (tptt) REVERT: S 51 ARG cc_start: 0.8622 (ttm-80) cc_final: 0.8232 (ttm-80) REVERT: S 63 THR cc_start: 0.8913 (m) cc_final: 0.8647 (p) REVERT: U 87 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.7788 (tptt) REVERT: W 83 ARG cc_start: 0.9361 (mtp85) cc_final: 0.9078 (mtp85) REVERT: W 87 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.7574 (tptt) REVERT: X 52 SER cc_start: 0.8955 (t) cc_final: 0.8622 (m) REVERT: X 87 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.7814 (tptt) REVERT: Y 51 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8114 (ttm110) REVERT: Y 87 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.7890 (tptt) REVERT: Z 63 THR cc_start: 0.9073 (m) cc_final: 0.8768 (p) REVERT: Z 87 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.7639 (tptt) REVERT: a 63 THR cc_start: 0.9169 (m) cc_final: 0.8965 (p) REVERT: a 87 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8571 (ptmt) outliers start: 160 outliers final: 100 residues processed: 704 average time/residue: 0.2500 time to fit residues: 287.8787 Evaluate side-chains 715 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 582 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 65 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 65 VAL Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 64 ILE Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 64 ILE Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain A1 residue 64 ILE Chi-restraints excluded: chain A1 residue 65 VAL Chi-restraints excluded: chain A1 residue 85 ILE Chi-restraints excluded: chain A2 residue 64 ILE Chi-restraints excluded: chain A2 residue 65 VAL Chi-restraints excluded: chain A2 residue 99 ILE Chi-restraints excluded: chain A3 residue 65 VAL Chi-restraints excluded: chain A4 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A6 residue 65 VAL Chi-restraints excluded: chain A7 residue 64 ILE Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 2 residue 65 VAL Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 54 LEU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 64 ILE Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain t residue 99 ILE Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 65 VAL Chi-restraints excluded: chain z residue 64 ILE Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain n residue 65 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 52 SER Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 94 SER Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 13 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 328 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.090577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.073005 restraints weight = 58032.395| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 1.94 r_work: 0.2659 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39537 Z= 0.140 Angle : 0.444 7.512 52923 Z= 0.231 Chirality : 0.037 0.166 6555 Planarity : 0.003 0.024 6072 Dihedral : 16.416 76.718 8220 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 4.29 % Allowed : 11.35 % Favored : 84.35 % 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 aren not related in a simple way. whole: 4.75 (0.12), residues: 4623 helix: 3.73 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.47 (0.20), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 2 51 TYR 0.006 0.001 TYR 1 80 PHE 0.007 0.001 PHE r 111 TRP 0.004 0.001 TRP F 93 Details of bonding type rmsd covalent geometry : bond 0.00350 (39537) covalent geometry : angle 0.44400 (52923) hydrogen bonds : bond 0.03491 ( 3134) hydrogen bonds : angle 2.90423 ( 9402) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 618 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8658 (ttp80) cc_final: 0.7832 (tpt170) REVERT: B 48 GLU cc_start: 0.8277 (tp30) cc_final: 0.7935 (tp30) REVERT: B 60 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8750 (mm-30) REVERT: F 63 THR cc_start: 0.9065 (m) cc_final: 0.8781 (p) REVERT: F 87 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.7531 (tptt) REVERT: G 87 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.7627 (tptt) REVERT: H 63 THR cc_start: 0.9089 (m) cc_final: 0.8570 (p) REVERT: I 87 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.7701 (tptt) REVERT: I 109 MET cc_start: 0.9309 (ttp) cc_final: 0.9103 (ttm) REVERT: J 86 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8007 (tt0) REVERT: J 87 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.7624 (tptt) REVERT: K 83 ARG cc_start: 0.9023 (mtp-110) cc_final: 0.8723 (mtp-110) REVERT: K 86 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7958 (pm20) REVERT: K 87 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8122 (tptt) REVERT: L 60 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8771 (mm-30) REVERT: M 45 GLN cc_start: 0.8468 (mt0) cc_final: 0.8194 (mt0) REVERT: M 63 THR cc_start: 0.9027 (m) cc_final: 0.8742 (p) REVERT: M 83 ARG cc_start: 0.9131 (mtp-110) cc_final: 0.8747 (mtm180) REVERT: 3 51 ARG cc_start: 0.8697 (ttp80) cc_final: 0.7183 (mtt-85) REVERT: 3 60 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8862 (mm-30) REVERT: 4 48 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7765 (tp30) REVERT: 4 49 LYS cc_start: 0.8923 (tttt) cc_final: 0.8639 (ttpt) REVERT: 4 51 ARG cc_start: 0.8456 (ttm-80) cc_final: 0.8040 (ttm-80) REVERT: 4 52 SER cc_start: 0.9235 (t) cc_final: 0.8777 (p) REVERT: 5 52 SER cc_start: 0.9338 (t) cc_final: 0.9038 (p) REVERT: 5 73 LEU cc_start: 0.9411 (tp) cc_final: 0.9141 (tp) REVERT: 5 87 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.7493 (tptt) REVERT: 6 87 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.7665 (tptt) REVERT: 8 87 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.7895 (tptt) REVERT: 9 87 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.7845 (tptt) REVERT: A6 45 GLN cc_start: 0.8296 (mt0) cc_final: 0.7981 (tt0) REVERT: A6 86 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8332 (pm20) REVERT: 0 48 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8256 (tp30) REVERT: 0 87 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8208 (ptpt) REVERT: 2 48 GLU cc_start: 0.8543 (tp30) cc_final: 0.8324 (tp30) REVERT: 2 60 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8805 (mm-30) REVERT: p 87 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.7295 (tptt) REVERT: q 87 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.7741 (tptt) REVERT: r 87 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8015 (tptt) REVERT: s 60 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8691 (mm-30) REVERT: s 87 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.7821 (tptt) REVERT: t 48 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8201 (tp30) REVERT: t 86 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8092 (pm20) REVERT: t 87 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.7780 (tptt) REVERT: t 88 ASP cc_start: 0.9063 (p0) cc_final: 0.8715 (p0) REVERT: u 87 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.7529 (tptt) REVERT: v 94 SER cc_start: 0.9417 (m) cc_final: 0.9153 (p) REVERT: x 99 ILE cc_start: 0.9451 (mt) cc_final: 0.9217 (mt) REVERT: y 48 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8124 (tm-30) REVERT: z 87 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.7930 (tptt) REVERT: c 63 THR cc_start: 0.8941 (m) cc_final: 0.8699 (p) REVERT: c 87 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.7348 (tptt) REVERT: d 48 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7521 (mt-10) REVERT: d 83 ARG cc_start: 0.9069 (mtp85) cc_final: 0.8737 (mtp85) REVERT: f 87 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.7850 (tptt) REVERT: g 63 THR cc_start: 0.8703 (m) cc_final: 0.8451 (p) REVERT: g 87 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.7875 (tptt) REVERT: h 87 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8781 (ptmt) REVERT: i 88 ASP cc_start: 0.9131 (p0) cc_final: 0.8846 (p0) REVERT: j 87 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.7995 (tptt) REVERT: k 87 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8013 (tptt) REVERT: l 87 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.7981 (tptt) REVERT: O 51 ARG cc_start: 0.8763 (ttp80) cc_final: 0.7537 (ttm170) REVERT: O 87 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.7663 (tptt) REVERT: P 52 SER cc_start: 0.9160 (t) cc_final: 0.8768 (p) REVERT: P 87 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7517 (tptt) REVERT: Q 87 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.7624 (tptt) REVERT: S 51 ARG cc_start: 0.8641 (ttm-80) cc_final: 0.8257 (ttm-80) REVERT: S 63 THR cc_start: 0.8870 (m) cc_final: 0.8634 (p) REVERT: U 87 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.7794 (tptt) REVERT: V 60 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8764 (mm-30) REVERT: W 83 ARG cc_start: 0.9357 (mtp85) cc_final: 0.9084 (mtp85) REVERT: W 87 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.7580 (tptt) REVERT: X 52 SER cc_start: 0.8956 (t) cc_final: 0.8622 (m) REVERT: X 87 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.7780 (tptt) REVERT: Y 51 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8125 (ttm110) REVERT: Y 87 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7897 (tptt) REVERT: Z 63 THR cc_start: 0.9073 (m) cc_final: 0.8765 (p) REVERT: Z 87 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.7652 (tptt) REVERT: a 63 THR cc_start: 0.9174 (m) cc_final: 0.8959 (p) REVERT: a 87 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8582 (ptpt) outliers start: 160 outliers final: 102 residues processed: 722 average time/residue: 0.2497 time to fit residues: 293.5765 Evaluate side-chains 729 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 594 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 4 residue 65 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 64 ILE Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 65 VAL Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 64 ILE Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 78 ILE Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 64 ILE Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain A1 residue 64 ILE Chi-restraints excluded: chain A1 residue 65 VAL Chi-restraints excluded: chain A1 residue 85 ILE Chi-restraints excluded: chain A2 residue 64 ILE Chi-restraints excluded: chain A2 residue 65 VAL Chi-restraints excluded: chain A2 residue 99 ILE Chi-restraints excluded: chain A3 residue 65 VAL Chi-restraints excluded: chain A4 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A6 residue 65 VAL Chi-restraints excluded: chain A7 residue 64 ILE Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 2 residue 65 VAL Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 54 LEU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 64 ILE Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain t residue 99 ILE Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 65 VAL Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 52 SER Chi-restraints excluded: chain c residue 55 GLU Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain c residue 104 VAL Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain n residue 65 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 52 SER Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 94 SER Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 250 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 58 optimal weight: 0.0170 chunk 327 optimal weight: 2.9990 chunk 395 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 312 optimal weight: 8.9990 chunk 268 optimal weight: 0.0670 chunk 255 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 392 optimal weight: 0.3980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN p 105 GLN y 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.092001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.073790 restraints weight = 57700.433| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.05 r_work: 0.2666 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39537 Z= 0.112 Angle : 0.426 6.811 52923 Z= 0.225 Chirality : 0.036 0.170 6555 Planarity : 0.003 0.038 6072 Dihedral : 16.209 71.275 8220 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 4.03 % Allowed : 11.51 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.93 (0.12), residues: 4623 helix: 3.84 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.49 (0.20), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 2 51 TYR 0.004 0.001 TYR s 80 PHE 0.004 0.001 PHE 1 90 TRP 0.004 0.001 TRP F 93 Details of bonding type rmsd covalent geometry : bond 0.00264 (39537) covalent geometry : angle 0.42625 (52923) hydrogen bonds : bond 0.03183 ( 3134) hydrogen bonds : angle 2.80919 ( 9402) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 625 time to evaluate : 1.373 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: B 48 GLU cc_start: 0.8261 (tp30) cc_final: 0.7910 (tp30) REVERT: B 60 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8766 (mm-30) REVERT: F 63 THR cc_start: 0.9047 (m) cc_final: 0.8757 (p) REVERT: F 87 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.7543 (tptt) REVERT: G 87 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.7621 (tptt) REVERT: H 63 THR cc_start: 0.9062 (m) cc_final: 0.8754 (p) REVERT: I 87 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.7681 (tptt) REVERT: J 86 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8031 (tt0) REVERT: J 87 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7578 (tptt) REVERT: K 83 ARG cc_start: 0.9024 (mtp-110) cc_final: 0.8509 (mtp-110) REVERT: K 86 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7953 (pm20) REVERT: K 87 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8074 (tptt) REVERT: L 60 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8777 (mm-30) REVERT: M 45 GLN cc_start: 0.8416 (mt0) cc_final: 0.8133 (mt0) REVERT: M 63 THR cc_start: 0.8984 (m) cc_final: 0.8704 (p) REVERT: M 83 ARG cc_start: 0.9137 (mtp-110) cc_final: 0.8762 (mtm180) REVERT: 3 51 ARG cc_start: 0.8688 (ttp80) cc_final: 0.7189 (mtt-85) REVERT: 4 48 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7760 (tp30) REVERT: 4 49 LYS cc_start: 0.8920 (tttt) cc_final: 0.8655 (ttpt) REVERT: 4 51 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.7993 (ttm-80) REVERT: 4 52 SER cc_start: 0.9228 (t) cc_final: 0.8783 (p) REVERT: 5 52 SER cc_start: 0.9311 (t) cc_final: 0.9099 (p) REVERT: 5 73 LEU cc_start: 0.9406 (tp) cc_final: 0.9156 (tp) REVERT: 5 87 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.7473 (tptt) REVERT: 6 87 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7591 (tptt) REVERT: 8 87 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7879 (tptt) REVERT: 9 87 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.7826 (tptt) REVERT: A6 45 GLN cc_start: 0.8239 (mt0) cc_final: 0.7875 (tt0) REVERT: A6 86 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8344 (pm20) REVERT: A7 63 THR cc_start: 0.9046 (m) cc_final: 0.8628 (p) REVERT: 0 48 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8185 (tp30) REVERT: 0 83 ARG cc_start: 0.9254 (mtp85) cc_final: 0.8978 (mtp85) REVERT: 0 87 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8232 (ptmt) REVERT: 2 51 ARG cc_start: 0.8923 (ttp80) cc_final: 0.8290 (ttm110) REVERT: p 87 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.7280 (tptt) REVERT: q 87 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.7791 (tptt) REVERT: r 87 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8056 (tptt) REVERT: s 60 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8720 (mm-30) REVERT: s 87 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.7802 (tptt) REVERT: t 86 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8106 (pm20) REVERT: t 87 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.7830 (tptt) REVERT: t 88 ASP cc_start: 0.9048 (p0) cc_final: 0.8615 (p0) REVERT: u 87 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7502 (tptt) REVERT: v 94 SER cc_start: 0.9412 (m) cc_final: 0.9166 (p) REVERT: x 99 ILE cc_start: 0.9430 (mt) cc_final: 0.9197 (mt) REVERT: y 48 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8033 (tm-30) REVERT: z 87 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.7941 (tptt) REVERT: c 63 THR cc_start: 0.8981 (m) cc_final: 0.8757 (p) REVERT: c 87 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.7334 (tptt) REVERT: d 48 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7481 (mt-10) REVERT: d 83 ARG cc_start: 0.9028 (mtp85) cc_final: 0.8697 (mtp85) REVERT: f 87 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.7838 (tptt) REVERT: g 63 THR cc_start: 0.8771 (m) cc_final: 0.8528 (p) REVERT: g 87 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.7856 (tptt) REVERT: h 87 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8761 (ptmt) REVERT: i 88 ASP cc_start: 0.9126 (p0) cc_final: 0.8850 (p0) REVERT: j 87 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8006 (tptt) REVERT: k 87 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.7991 (tptt) REVERT: l 87 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.7979 (tptt) REVERT: o 63 THR cc_start: 0.8972 (m) cc_final: 0.8613 (p) REVERT: o 83 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.7112 (mmp80) REVERT: O 51 ARG cc_start: 0.8734 (ttp80) cc_final: 0.7522 (ttm170) REVERT: O 87 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.7710 (tptt) REVERT: P 52 SER cc_start: 0.9144 (t) cc_final: 0.8772 (p) REVERT: P 87 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7539 (tptt) REVERT: Q 87 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7620 (tptt) REVERT: S 51 ARG cc_start: 0.8619 (ttm-80) cc_final: 0.8278 (ttm-80) REVERT: S 63 THR cc_start: 0.8816 (m) cc_final: 0.8536 (p) REVERT: U 87 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.7776 (tptt) REVERT: V 60 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8749 (mm-30) REVERT: W 83 ARG cc_start: 0.9353 (mtp85) cc_final: 0.9078 (mtp85) REVERT: W 87 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.7570 (tptt) REVERT: X 52 SER cc_start: 0.8911 (t) cc_final: 0.8579 (m) REVERT: X 87 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.7771 (tptt) REVERT: Y 87 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.7874 (tptt) REVERT: Z 63 THR cc_start: 0.9051 (m) cc_final: 0.8756 (p) REVERT: Z 87 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.7650 (tptt) REVERT: a 87 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8599 (ptpt) outliers start: 150 outliers final: 98 residues processed: 717 average time/residue: 0.2395 time to fit residues: 281.3404 Evaluate side-chains 735 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 604 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 4 residue 65 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 65 VAL Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 64 ILE Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 78 ILE Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain A1 residue 64 ILE Chi-restraints excluded: chain A1 residue 65 VAL Chi-restraints excluded: chain A1 residue 85 ILE Chi-restraints excluded: chain A2 residue 64 ILE Chi-restraints excluded: chain A2 residue 65 VAL Chi-restraints excluded: chain A2 residue 99 ILE Chi-restraints excluded: chain A3 residue 65 VAL Chi-restraints excluded: chain A4 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A6 residue 65 VAL Chi-restraints excluded: chain A7 residue 64 ILE Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 2 residue 65 VAL Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 64 ILE Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain t residue 99 ILE Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 65 VAL Chi-restraints excluded: chain z residue 64 ILE Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain n residue 65 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 52 SER Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 52 SER Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 94 SER Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 52 SER Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 394 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 188 optimal weight: 0.0970 chunk 324 optimal weight: 0.9980 chunk 303 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 410 optimal weight: 0.0070 chunk 377 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.092675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.075240 restraints weight = 57152.720| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.91 r_work: 0.2709 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 39537 Z= 0.102 Angle : 0.416 7.136 52923 Z= 0.221 Chirality : 0.036 0.159 6555 Planarity : 0.003 0.027 6072 Dihedral : 15.948 64.655 8220 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.70 % Allowed : 12.05 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.06 (0.12), residues: 4623 helix: 3.94 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.51 (0.19), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 2 51 TYR 0.004 0.001 TYR q 80 PHE 0.005 0.000 PHE c 111 TRP 0.005 0.001 TRP a 93 Details of bonding type rmsd covalent geometry : bond 0.00228 (39537) covalent geometry : angle 0.41644 (52923) hydrogen bonds : bond 0.03014 ( 3134) hydrogen bonds : angle 2.74902 ( 9402) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9246 Ramachandran restraints generated. 4623 Oldfield, 0 Emsley, 4623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 629 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.8219 (tp30) cc_final: 0.7879 (tp30) REVERT: B 60 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8748 (mm-30) REVERT: F 63 THR cc_start: 0.9039 (m) cc_final: 0.8779 (p) REVERT: F 87 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.7626 (tptt) REVERT: G 87 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.7634 (tptt) REVERT: H 63 THR cc_start: 0.9014 (m) cc_final: 0.8774 (p) REVERT: I 87 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.7694 (tptt) REVERT: J 86 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7963 (tt0) REVERT: J 87 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7592 (tptt) REVERT: K 83 ARG cc_start: 0.8889 (mtp-110) cc_final: 0.8452 (mtp-110) REVERT: K 86 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7947 (pm20) REVERT: K 87 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8106 (tptt) REVERT: L 60 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8778 (mm-30) REVERT: M 45 GLN cc_start: 0.8438 (mt0) cc_final: 0.8192 (mt0) REVERT: M 63 THR cc_start: 0.8924 (m) cc_final: 0.8681 (p) REVERT: M 83 ARG cc_start: 0.9128 (mtp-110) cc_final: 0.8761 (mtm180) REVERT: 3 51 ARG cc_start: 0.8674 (ttp80) cc_final: 0.7147 (mtt-85) REVERT: 3 60 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8399 (mm-30) REVERT: 4 48 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7703 (tp30) REVERT: 4 49 LYS cc_start: 0.8905 (tttt) cc_final: 0.8647 (ttpt) REVERT: 4 51 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.7957 (ttm-80) REVERT: 4 52 SER cc_start: 0.9210 (t) cc_final: 0.8781 (p) REVERT: 5 73 LEU cc_start: 0.9385 (tp) cc_final: 0.9161 (tp) REVERT: 5 87 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.7481 (tptt) REVERT: 6 87 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.7567 (tptt) REVERT: 8 87 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.7887 (tptt) REVERT: 9 87 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.7828 (tptt) REVERT: A6 45 GLN cc_start: 0.8237 (mt0) cc_final: 0.7875 (tt0) REVERT: A6 86 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8329 (pm20) REVERT: A7 63 THR cc_start: 0.9013 (m) cc_final: 0.8585 (p) REVERT: 0 48 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8068 (tp30) REVERT: 0 87 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8247 (ptmt) REVERT: 2 51 ARG cc_start: 0.8912 (ttp80) cc_final: 0.8364 (ttm110) REVERT: p 87 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.7275 (tptt) REVERT: q 87 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.7789 (tptt) REVERT: r 87 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8054 (tptt) REVERT: s 87 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.7763 (tptt) REVERT: t 86 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8055 (pm20) REVERT: t 87 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.7870 (tptt) REVERT: t 88 ASP cc_start: 0.8978 (p0) cc_final: 0.8663 (p0) REVERT: u 87 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.7492 (tptt) REVERT: v 94 SER cc_start: 0.9378 (m) cc_final: 0.9156 (p) REVERT: x 99 ILE cc_start: 0.9425 (mt) cc_final: 0.9199 (mt) REVERT: y 48 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8132 (tm-30) REVERT: z 87 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.7925 (tptt) REVERT: c 63 THR cc_start: 0.8943 (m) cc_final: 0.8741 (p) REVERT: c 86 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8157 (tp30) REVERT: c 87 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.7279 (tptt) REVERT: d 48 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7468 (mt-10) REVERT: d 83 ARG cc_start: 0.8998 (mtp85) cc_final: 0.8664 (mtp85) REVERT: f 87 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.7826 (tptt) REVERT: g 63 THR cc_start: 0.8764 (m) cc_final: 0.8550 (p) REVERT: g 87 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8050 (tptt) REVERT: h 87 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8670 (ptmt) REVERT: i 48 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7417 (mp0) REVERT: i 88 ASP cc_start: 0.9111 (p0) cc_final: 0.8846 (p0) REVERT: j 87 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.7999 (tptt) REVERT: k 87 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8022 (tptt) REVERT: l 87 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.7938 (tptt) REVERT: o 83 ARG cc_start: 0.8750 (mtp-110) cc_final: 0.7079 (tpp-160) REVERT: O 51 ARG cc_start: 0.8706 (ttp80) cc_final: 0.7507 (ttm170) REVERT: O 87 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.7693 (tptt) REVERT: P 52 SER cc_start: 0.9121 (t) cc_final: 0.8773 (p) REVERT: P 87 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7523 (tptt) REVERT: Q 87 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7620 (tptt) REVERT: S 51 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8269 (ttm-80) REVERT: S 63 THR cc_start: 0.8722 (m) cc_final: 0.8520 (p) REVERT: U 86 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8351 (mm-30) REVERT: U 87 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.7800 (tptt) REVERT: V 60 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8804 (mm-30) REVERT: W 83 ARG cc_start: 0.9336 (mtp85) cc_final: 0.9069 (mtp85) REVERT: W 87 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.7536 (tptt) REVERT: X 52 SER cc_start: 0.8886 (t) cc_final: 0.8616 (m) REVERT: X 87 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.7818 (tptt) REVERT: Y 87 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7878 (tptt) REVERT: Z 63 THR cc_start: 0.9017 (m) cc_final: 0.8743 (p) REVERT: Z 87 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.7670 (tptt) REVERT: a 87 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8609 (ptmt) REVERT: b 105 GLN cc_start: 0.9362 (mp10) cc_final: 0.9109 (mp10) outliers start: 138 outliers final: 96 residues processed: 712 average time/residue: 0.2555 time to fit residues: 297.5833 Evaluate side-chains 728 residues out of total 3726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 599 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain G residue 87 LYS Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 87 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 87 LYS Chi-restraints excluded: chain K residue 87 LYS Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 65 VAL Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 3 residue 65 VAL Chi-restraints excluded: chain 4 residue 65 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 87 LYS Chi-restraints excluded: chain 6 residue 52 SER Chi-restraints excluded: chain 6 residue 65 VAL Chi-restraints excluded: chain 6 residue 87 LYS Chi-restraints excluded: chain 7 residue 64 ILE Chi-restraints excluded: chain 7 residue 65 VAL Chi-restraints excluded: chain 7 residue 78 ILE Chi-restraints excluded: chain 8 residue 64 ILE Chi-restraints excluded: chain 8 residue 87 LYS Chi-restraints excluded: chain 9 residue 64 ILE Chi-restraints excluded: chain 9 residue 87 LYS Chi-restraints excluded: chain 9 residue 112 THR Chi-restraints excluded: chain A1 residue 64 ILE Chi-restraints excluded: chain A1 residue 65 VAL Chi-restraints excluded: chain A1 residue 85 ILE Chi-restraints excluded: chain A2 residue 64 ILE Chi-restraints excluded: chain A2 residue 65 VAL Chi-restraints excluded: chain A2 residue 99 ILE Chi-restraints excluded: chain A3 residue 65 VAL Chi-restraints excluded: chain A4 residue 65 VAL Chi-restraints excluded: chain A5 residue 65 VAL Chi-restraints excluded: chain A6 residue 65 VAL Chi-restraints excluded: chain A7 residue 64 ILE Chi-restraints excluded: chain 0 residue 65 VAL Chi-restraints excluded: chain 0 residue 87 LYS Chi-restraints excluded: chain 0 residue 112 THR Chi-restraints excluded: chain 2 residue 65 VAL Chi-restraints excluded: chain p residue 64 ILE Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 87 LYS Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 87 LYS Chi-restraints excluded: chain s residue 64 ILE Chi-restraints excluded: chain s residue 87 LYS Chi-restraints excluded: chain t residue 64 ILE Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain t residue 87 LYS Chi-restraints excluded: chain t residue 99 ILE Chi-restraints excluded: chain u residue 64 ILE Chi-restraints excluded: chain u residue 65 VAL Chi-restraints excluded: chain u residue 87 LYS Chi-restraints excluded: chain v residue 64 ILE Chi-restraints excluded: chain v residue 65 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain y residue 45 GLN Chi-restraints excluded: chain y residue 64 ILE Chi-restraints excluded: chain y residue 65 VAL Chi-restraints excluded: chain z residue 64 ILE Chi-restraints excluded: chain z residue 87 LYS Chi-restraints excluded: chain c residue 87 LYS Chi-restraints excluded: chain d residue 65 VAL Chi-restraints excluded: chain e residue 52 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain f residue 52 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 87 LYS Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 65 VAL Chi-restraints excluded: chain g residue 87 LYS Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 87 LYS Chi-restraints excluded: chain i residue 64 ILE Chi-restraints excluded: chain i residue 87 LYS Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 87 LYS Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 87 LYS Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain n residue 65 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 87 LYS Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 87 LYS Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain S residue 52 SER Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 64 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 52 SER Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 87 LYS Chi-restraints excluded: chain W residue 94 SER Chi-restraints excluded: chain X residue 87 LYS Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Y residue 65 VAL Chi-restraints excluded: chain Y residue 87 LYS Chi-restraints excluded: chain Z residue 52 SER Chi-restraints excluded: chain Z residue 64 ILE Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 87 LYS Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 87 LYS Chi-restraints excluded: chain b residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 128 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 354 optimal weight: 0.5980 chunk 259 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3089 r_free = 0.3089 target = 0.091159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.073665 restraints weight = 58219.630| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 1.99 r_work: 0.2649 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39537 Z= 0.159 Angle : 0.460 7.788 52923 Z= 0.238 Chirality : 0.038 0.153 6555 Planarity : 0.003 0.033 6072 Dihedral : 15.829 59.489 8220 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.54 % Allowed : 12.75 % Favored : 83.71 % 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 aren not related in a simple way. whole: 4.78 (0.12), residues: 4623 helix: 3.74 (0.07), residues: 4209 sheet: None (None), residues: 0 loop : -4.46 (0.20), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 2 51 TYR 0.011 0.001 TYR q 80 PHE 0.007 0.001 PHE r 111 TRP 0.004 0.001 TRP 3 93 Details of bonding type rmsd covalent geometry : bond 0.00404 (39537) covalent geometry : angle 0.45977 (52923) hydrogen bonds : bond 0.03567 ( 3134) hydrogen bonds : angle 2.92650 ( 9402) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8790.72 seconds wall clock time: 151 minutes 33.08 seconds (9093.08 seconds total)