Starting phenix.real_space_refine on Tue Aug 4 18:24:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdw_71546/08_2026/9pdw_71546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdw_71546/08_2026/9pdw_71546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pdw_71546/08_2026/9pdw_71546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdw_71546/08_2026/9pdw_71546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pdw_71546/08_2026/9pdw_71546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdw_71546/08_2026/9pdw_71546.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.034 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: 3 Type Number sf(0) Gaussians C 4275 2.51 5 N 825 2.21 5 O 825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5925 Number of models: 1 Model: "" Number of chains: 150 Chain: "M" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AG" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AI" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AK" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AO" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AW" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AQ" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AY" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AS" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AU" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AT" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "AT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Aa" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Aa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ad" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Ad" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ab" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'ACE': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 7} Chain: "Ab" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.68, per 1000 atoms: 0.28 Number of scatterers: 5925 At special positions: 0 Unit cell: (87.15, 87.98, 64.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 825 8.00 N 825 7.00 C 4275 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=75, symmetry=0 Number of additional bonds: simple=75, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 99.8 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1050 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'V' and resid 3 through 8 Processing sheet with id=AA2, first strand: chain 'W' and resid 3 through 8 Processing sheet with id=AA3, first strand: chain 'g' and resid 3 through 8 Processing sheet with id=AA4, first strand: chain 'e' and resid 3 through 8 removed outlier: 6.366A pdb=" N PHE r 4 " --> pdb=" O GLY 6 5 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LYS 6 7 " --> pdb=" O PHE r 4 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE r 6 " --> pdb=" O LYS 6 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'u' and resid 6 through 7 removed outlier: 3.597A pdb=" N PHE u 6 " --> pdb=" O PHE 2 4 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE 2 4 " --> pdb=" O PHE u 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '9' and resid 6 through 7 removed outlier: 3.653A pdb=" N PHE 9 6 " --> pdb=" O PHEAF 4 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHEAF 4 " --> pdb=" O PHE 9 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'AA' and resid 6 through 7 removed outlier: 3.676A pdb=" N PHEAA 6 " --> pdb=" O PHEAH 4 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 474 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: 1.04 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.26: 629 1.26 - 1.34: 719 1.34 - 1.41: 1802 1.41 - 1.49: 677 1.49 - 1.56: 2248 Bond restraints: 6075 Sorted by residual: bond pdb=" C ACE y 1 " pdb=" N PHE y 2 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C ACEAK 1 " pdb=" N PHEAK 2 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C ACE j 1 " pdb=" N PHE j 2 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C ACEAd 1 " pdb=" N PHEAd 2 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C ACEAa 1 " pdb=" N PHEAa 2 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.95e+01 ... (remaining 6070 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 6866 1.60 - 3.21: 559 3.21 - 4.81: 303 4.81 - 6.41: 48 6.41 - 8.01: 24 Bond angle restraints: 7800 Sorted by residual: angle pdb=" CA PHEAH 8 " pdb=" C PHEAH 8 " pdb=" N GLUAH 9 " ideal model delta sigma weight residual 119.46 115.73 3.73 6.10e-01 2.69e+00 3.74e+01 angle pdb=" CA PHE 2 8 " pdb=" C PHE 2 8 " pdb=" N GLU 2 9 " ideal model delta sigma weight residual 119.46 115.75 3.71 6.10e-01 2.69e+00 3.70e+01 angle pdb=" CA PHEAY 8 " pdb=" C PHEAY 8 " pdb=" N GLUAY 9 " ideal model delta sigma weight residual 119.46 115.77 3.69 6.10e-01 2.69e+00 3.67e+01 angle pdb=" CA PHEAG 8 " pdb=" C PHEAG 8 " pdb=" N GLUAG 9 " ideal model delta sigma weight residual 119.46 115.77 3.69 6.10e-01 2.69e+00 3.66e+01 angle pdb=" CA PHE l 8 " pdb=" C PHE l 8 " pdb=" N GLU l 9 " ideal model delta sigma weight residual 119.46 115.78 3.68 6.10e-01 2.69e+00 3.64e+01 ... (remaining 7795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 2827 36.00 - 72.00: 249 72.00 - 108.00: 17 108.00 - 144.00: 0 144.00 - 180.00: 57 Dihedral angle restraints: 3150 sinusoidal: 1575 harmonic: 1575 Sorted by residual: dihedral pdb=" CH3 ACE c 1 " pdb=" C ACE c 1 " pdb=" N PHE c 2 " pdb=" CA PHE c 2 " ideal model delta sinusoidal sigma weight residual 180.00 0.00 180.00 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACEAU 1 " pdb=" C ACEAU 1 " pdb=" N PHEAU 2 " pdb=" CA PHEAU 2 " ideal model delta sinusoidal sigma weight residual -180.00 -0.00 -180.00 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACEAS 1 " pdb=" C ACEAS 1 " pdb=" N PHEAS 2 " pdb=" CA PHEAS 2 " ideal model delta sinusoidal sigma weight residual -180.00 -0.01 -179.99 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 3147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 474 0.050 - 0.099: 17 0.099 - 0.149: 15 0.149 - 0.199: 2 0.199 - 0.249: 17 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA GLU 3 9 " pdb=" N GLU 3 9 " pdb=" C GLU 3 9 " pdb=" CB GLU 3 9 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA GLUAI 9 " pdb=" N GLUAI 9 " pdb=" C GLUAI 9 " pdb=" CB GLUAI 9 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA GLU 2 9 " pdb=" N GLU 2 9 " pdb=" C GLU 2 9 " pdb=" CB GLU 2 9 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 522 not shown) Planarity restraints: 975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHEAD 8 " -0.005 2.00e-02 2.50e+03 8.96e-03 1.41e+00 pdb=" CG PHEAD 8 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHEAD 8 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHEAD 8 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHEAD 8 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEAD 8 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHEAD 8 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEAL 4 " -0.005 2.00e-02 2.50e+03 8.34e-03 1.22e+00 pdb=" CG PHEAL 4 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHEAL 4 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEAL 4 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHEAL 4 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHEAL 4 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHEAL 4 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHEAT 6 " -0.006 2.00e-02 2.50e+03 7.55e-03 9.98e-01 pdb=" CG PHEAT 6 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHEAT 6 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHEAT 6 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHEAT 6 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHEAT 6 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHEAT 6 " 0.000 2.00e-02 2.50e+03 ... (remaining 972 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2135 2.85 - 3.36: 3894 3.36 - 3.88: 10179 3.88 - 4.39: 12009 4.39 - 4.90: 21052 Nonbonded interactions: 49269 Sorted by model distance: nonbonded pdb=" NZ LYS X 7 " pdb=" OE2 GLU X 9 " model vdw 2.339 3.120 nonbonded pdb=" NZ LYSAH 7 " pdb=" OE2 GLUAH 9 " model vdw 2.345 3.120 nonbonded pdb=" NZ LYS 2 7 " pdb=" OE2 GLU 2 9 " model vdw 2.376 3.120 nonbonded pdb=" NZ LYSAX 7 " pdb=" OE2 GLUAX 9 " model vdw 2.377 3.120 nonbonded pdb=" NZ LYS W 3 " pdb=" OE2 GLU w 9 " model vdw 2.390 3.120 ... (remaining 49264 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' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AR' selection = chain 'AS' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'Aa' selection = chain 'Ab' selection = chain 'Ad' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.760 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 : 0.017 0.127 6150 Z= 0.967 Angle : 1.247 8.014 7800 Z= 0.722 Chirality : 0.050 0.249 525 Planarity : 0.001 0.009 975 Dihedral : 36.832 179.999 2100 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 7.24 % Allowed : 36.95 % Favored : 55.81 % 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 are not related in a simple way. whole: -3.98 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 PHEAD 8 Details of bonding type rmsd/Z covalent geometry : bond 0.01594 / 0.79 ( 6075) covalent geometry : angle 1.24672 / 0.72 ( 7800) hydrogen bonds : bond 0.16693 / 9.20 ( 158) hydrogen bonds : angle 7.97437 / 5.09 ( 474) Misc. bond : bond 0.05113 / 2.83 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.291 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: g 9 GLU cc_start: 0.8131 (tt0) cc_final: 0.6739 (pm20) REVERT: R 3 LYS cc_start: 0.7197 (mppt) cc_final: 0.6933 (ttmm) REVERT: o 9 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: z 7 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7192 (mmtt) REVERT: 8 9 GLU cc_start: 0.7679 (tt0) cc_final: 0.7384 (tt0) REVERT: AF 7 LYS cc_start: 0.7595 (mmtt) cc_final: 0.7225 (mmpt) REVERT: AH 2 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.6201 (m-80) REVERT: AB 3 LYS cc_start: 0.7338 (mptt) cc_final: 0.7050 (mppt) REVERT: AI 2 PHE cc_start: 0.4886 (OUTLIER) cc_final: 0.4396 (t80) REVERT: AN 7 LYS cc_start: 0.8044 (tptm) cc_final: 0.7401 (tptp) REVERT: AX 2 PHE cc_start: 0.5535 (OUTLIER) cc_final: 0.5284 (m-80) REVERT: AR 7 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6878 (mmtt) REVERT: Ab 9 GLU cc_start: 0.7161 (tt0) cc_final: 0.6895 (tt0) outliers start: 38 outliers final: 5 residues processed: 141 average time/residue: 0.5137 time to fit residues: 75.2946 Evaluate side-chains 105 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain 0 residue 7 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AB residue 9 GLU Chi-restraints excluded: chain AI residue 2 PHE Chi-restraints excluded: chain AP residue 7 LYS Chi-restraints excluded: chain AX residue 2 PHE Chi-restraints excluded: chain AR residue 9 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.7980 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.087907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.068081 restraints weight = 12119.330| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.39 r_work: 0.2695 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.8019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.274 6150 Z= 3.200 Angle : 2.812 22.794 7800 Z= 1.429 Chirality : 0.152 0.520 525 Planarity : 0.016 0.102 975 Dihedral : 48.082 178.976 702 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 35.39 Ramachandran Plot: Outliers : 2.67 % Allowed : 29.11 % Favored : 68.22 % Rotamer: Outliers : 12.00 % Allowed : 24.38 % Favored : 63.62 % Cbeta Deviations : 1.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.26 (0.24), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.76 (0.18), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.089 0.010 PHEAX 2 Details of bonding type rmsd/Z covalent geometry : bond 0.08023 / 3.22 ( 6075) covalent geometry : angle 2.81173 / 1.43 ( 7800) hydrogen bonds : bond 0.07471 / 4.20 ( 158) hydrogen bonds : angle 5.43186 / 3.50 ( 474) Misc. bond : bond 0.01201 / 0.70 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 LYS cc_start: 0.8674 (mppt) cc_final: 0.7976 (mtpm) REVERT: M 7 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8594 (ptpp) REVERT: P 9 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6750 (pm20) REVERT: b 3 LYS cc_start: 0.7905 (tmtt) cc_final: 0.7686 (tmtt) REVERT: b 9 GLU cc_start: 0.8244 (mp0) cc_final: 0.7656 (mp0) REVERT: Q 9 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: R 3 LYS cc_start: 0.7878 (mppt) cc_final: 0.7644 (ttmm) REVERT: S 7 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7920 (mmtt) REVERT: m 7 LYS cc_start: 0.8759 (mtpm) cc_final: 0.8539 (mtpp) REVERT: m 9 GLU cc_start: 0.8562 (mp0) cc_final: 0.8281 (mp0) REVERT: U 7 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8247 (ptmm) REVERT: z 3 LYS cc_start: 0.8070 (tmtt) cc_final: 0.7747 (tmtt) REVERT: t 3 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7381 (mtpm) REVERT: 1 3 LYS cc_start: 0.7585 (tmtt) cc_final: 0.7177 (tmtt) REVERT: 1 9 GLU cc_start: 0.8599 (mp0) cc_final: 0.7938 (mp0) REVERT: u 7 LYS cc_start: 0.8537 (tmtp) cc_final: 0.8186 (tmtp) REVERT: 2 9 GLU cc_start: 0.8461 (mp0) cc_final: 0.8088 (mp0) REVERT: v 3 LYS cc_start: 0.8590 (mptt) cc_final: 0.7734 (mtpm) REVERT: 3 7 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8173 (mptm) REVERT: AF 9 GLU cc_start: 0.8553 (mp0) cc_final: 0.8311 (mp0) REVERT: 0 3 LYS cc_start: 0.7916 (mppt) cc_final: 0.7369 (mtpm) REVERT: 0 7 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7301 (ptpt) REVERT: AG 2 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8225 (m-10) REVERT: AG 9 GLU cc_start: 0.8162 (mp0) cc_final: 0.7597 (mp0) REVERT: AA 3 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7702 (mtpm) REVERT: AH 3 LYS cc_start: 0.8457 (tmtt) cc_final: 0.8161 (tmtt) REVERT: AB 7 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7019 (ptpp) REVERT: AC 9 GLU cc_start: 0.9326 (tt0) cc_final: 0.8996 (tt0) REVERT: AJ 7 LYS cc_start: 0.9028 (ptmm) cc_final: 0.8816 (ptmt) REVERT: AM 9 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8983 (tt0) REVERT: AO 9 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: AV 7 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8322 (mttm) REVERT: AP 3 LYS cc_start: 0.7715 (mppt) cc_final: 0.6822 (tmtp) REVERT: AP 7 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7505 (ptpt) REVERT: AW 6 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8451 (p90) REVERT: AQ 7 LYS cc_start: 0.8731 (mtpm) cc_final: 0.8501 (mtpm) REVERT: AX 9 GLU cc_start: 0.8274 (mp0) cc_final: 0.7982 (mp0) REVERT: AY 9 GLU cc_start: 0.8076 (mp0) cc_final: 0.7768 (mp0) REVERT: AU 7 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.5891 (tppt) REVERT: Ab 9 GLU cc_start: 0.9098 (tt0) cc_final: 0.8894 (tt0) outliers start: 63 outliers final: 22 residues processed: 158 average time/residue: 0.8313 time to fit residues: 134.4551 Evaluate side-chains 152 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain V residue 7 LYS Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain S residue 9 GLU Chi-restraints excluded: chain n residue 7 LYS Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain p residue 9 GLU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain U residue 7 LYS Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain u residue 9 GLU Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 3 residue 7 LYS Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 0 residue 7 LYS Chi-restraints excluded: chain AG residue 2 PHE Chi-restraints excluded: chain AG residue 6 PHE Chi-restraints excluded: chain AA residue 3 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AB residue 7 LYS Chi-restraints excluded: chain AE residue 9 GLU Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AO residue 9 GLU Chi-restraints excluded: chain AV residue 7 LYS Chi-restraints excluded: chain AP residue 7 LYS Chi-restraints excluded: chain AW residue 6 PHE Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.066174 restraints weight = 13612.307| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.45 r_work: 0.2650 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.8695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.304 6150 Z= 3.178 Angle : 2.835 25.324 7800 Z= 1.426 Chirality : 0.158 0.485 525 Planarity : 0.014 0.052 975 Dihedral : 47.170 179.717 692 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 39.93 Ramachandran Plot: Outliers : 1.11 % Allowed : 37.56 % Favored : 61.33 % Rotamer: Outliers : 14.48 % Allowed : 22.86 % Favored : 62.67 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.53 (0.25), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.97 (0.19), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.093 0.009 PHE n 6 Details of bonding type rmsd/Z covalent geometry : bond 0.07962 / 3.20 ( 6075) covalent geometry : angle 2.83490 / 1.43 ( 7800) hydrogen bonds : bond 0.08093 / 4.51 ( 158) hydrogen bonds : angle 5.56690 / 3.52 ( 474) Misc. bond : bond 0.01161 / 0.68 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 128 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7871 (mtpm) REVERT: M 7 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8458 (ttpp) REVERT: M 9 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: P 7 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7957 (mmtt) REVERT: b 3 LYS cc_start: 0.7985 (tmtt) cc_final: 0.7620 (tmtt) REVERT: b 9 GLU cc_start: 0.8243 (mp0) cc_final: 0.7810 (mp0) REVERT: Q 9 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: k 3 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8316 (mtpp) REVERT: k 9 GLU cc_start: 0.7977 (mp0) cc_final: 0.7628 (mp0) REVERT: R 3 LYS cc_start: 0.7963 (mppt) cc_final: 0.7440 (ttmm) REVERT: S 7 LYS cc_start: 0.8259 (mmtt) cc_final: 0.8005 (mptt) REVERT: T 3 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.7988 (mtpm) REVERT: o 7 LYS cc_start: 0.9042 (tttt) cc_final: 0.8698 (tttm) REVERT: z 9 GLU cc_start: 0.8413 (mp0) cc_final: 0.7918 (mp0) REVERT: t 3 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7383 (mtpm) REVERT: t 7 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7629 (ptpt) REVERT: 1 3 LYS cc_start: 0.7748 (tmtt) cc_final: 0.7165 (tmtt) REVERT: u 7 LYS cc_start: 0.8677 (tmtp) cc_final: 0.8197 (tmtt) REVERT: 2 2 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8715 (m-10) REVERT: 2 9 GLU cc_start: 0.8461 (mp0) cc_final: 0.8217 (mp0) REVERT: v 3 LYS cc_start: 0.8626 (mptt) cc_final: 0.7826 (mtpm) REVERT: 9 3 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7506 (mtpm) REVERT: 0 3 LYS cc_start: 0.7995 (mppt) cc_final: 0.7569 (mtpm) REVERT: 0 7 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7437 (ptpt) REVERT: AG 2 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8338 (m-10) REVERT: AA 3 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7936 (mtpm) REVERT: AA 7 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8642 (ttmm) REVERT: AH 9 GLU cc_start: 0.8267 (mp0) cc_final: 0.7833 (mp0) REVERT: AB 7 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7145 (ptpp) REVERT: AN 7 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8819 (tttt) REVERT: AN 9 GLU cc_start: 0.9258 (tt0) cc_final: 0.9056 (tt0) REVERT: AM 7 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8983 (tptt) REVERT: AO 9 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: AV 7 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8370 (mttm) REVERT: AP 3 LYS cc_start: 0.7588 (mppt) cc_final: 0.7361 (mtpm) REVERT: AP 7 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7517 (ptpt) REVERT: AQ 7 LYS cc_start: 0.8881 (mtpm) cc_final: 0.8669 (mtpm) REVERT: AX 7 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8752 (mtpp) REVERT: AY 9 GLU cc_start: 0.8178 (mp0) cc_final: 0.7729 (mp0) REVERT: AU 7 LYS cc_start: 0.6748 (OUTLIER) cc_final: 0.5910 (tppt) REVERT: AT 9 GLU cc_start: 0.9281 (tt0) cc_final: 0.9012 (tt0) REVERT: Aa 7 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8592 (tptp) REVERT: Ad 7 LYS cc_start: 0.8910 (ptmt) cc_final: 0.7237 (tptt) REVERT: Ab 9 GLU cc_start: 0.9121 (tt0) cc_final: 0.8895 (tt0) outliers start: 76 outliers final: 30 residues processed: 169 average time/residue: 0.8402 time to fit residues: 145.3618 Evaluate side-chains 177 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain P residue 7 LYS Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain X residue 9 GLU Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain R residue 9 GLU Chi-restraints excluded: chain l residue 7 LYS Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain m residue 2 PHE Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain n residue 6 PHE Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain p residue 9 GLU Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain z residue 6 PHE Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain u residue 3 LYS Chi-restraints excluded: chain u residue 9 GLU Chi-restraints excluded: chain 2 residue 2 PHE Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain AF residue 7 LYS Chi-restraints excluded: chain 0 residue 7 LYS Chi-restraints excluded: chain AG residue 2 PHE Chi-restraints excluded: chain AG residue 4 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AA residue 2 PHE Chi-restraints excluded: chain AA residue 3 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AB residue 7 LYS Chi-restraints excluded: chain AE residue 9 GLU Chi-restraints excluded: chain AN residue 7 LYS Chi-restraints excluded: chain AM residue 7 LYS Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AO residue 9 GLU Chi-restraints excluded: chain AV residue 7 LYS Chi-restraints excluded: chain AP residue 7 LYS Chi-restraints excluded: chain AX residue 2 PHE Chi-restraints excluded: chain AX residue 7 LYS Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Chi-restraints excluded: chain Aa residue 7 LYS Chi-restraints excluded: chain Aa residue 9 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.085483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.065786 restraints weight = 14067.205| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.47 r_work: 0.2639 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.9072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.300 6150 Z= 3.171 Angle : 2.868 25.126 7800 Z= 1.437 Chirality : 0.160 0.487 525 Planarity : 0.013 0.048 975 Dihedral : 47.564 179.983 689 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 41.51 Ramachandran Plot: Outliers : 1.56 % Allowed : 37.78 % Favored : 60.67 % Rotamer: Outliers : 16.00 % Allowed : 24.57 % Favored : 59.43 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.51 (0.25), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.96 (0.19), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.091 0.009 PHE n 6 Details of bonding type rmsd/Z covalent geometry : bond 0.07946 / 3.19 ( 6075) covalent geometry : angle 2.86782 / 1.44 ( 7800) hydrogen bonds : bond 0.08362 / 4.67 ( 158) hydrogen bonds : angle 5.75602 / 3.63 ( 474) Misc. bond : bond 0.01150 / 0.67 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 122 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7931 (mtpt) REVERT: M 9 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: P 7 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8236 (mptt) REVERT: b 3 LYS cc_start: 0.7960 (tmtt) cc_final: 0.7601 (tmtt) REVERT: b 4 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.8731 (p90) REVERT: b 9 GLU cc_start: 0.8210 (mp0) cc_final: 0.7959 (mp0) REVERT: Q 9 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: k 3 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8309 (mtpp) REVERT: k 9 GLU cc_start: 0.7892 (mp0) cc_final: 0.7446 (mp0) REVERT: T 3 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7981 (mptt) REVERT: o 7 LYS cc_start: 0.9067 (tttt) cc_final: 0.8806 (tttm) REVERT: t 3 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7692 (tppp) REVERT: t 7 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7364 (mptp) REVERT: 1 3 LYS cc_start: 0.7764 (tmtt) cc_final: 0.7126 (tmtt) REVERT: u 7 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8149 (tmtt) REVERT: 2 2 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8832 (m-10) REVERT: 2 9 GLU cc_start: 0.8442 (mp0) cc_final: 0.8209 (mp0) REVERT: v 3 LYS cc_start: 0.8602 (mptt) cc_final: 0.8314 (mptt) REVERT: 3 7 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.7941 (mmtm) REVERT: 6 9 GLU cc_start: 0.9197 (tt0) cc_final: 0.8761 (tt0) REVERT: 9 3 LYS cc_start: 0.8095 (tmtt) cc_final: 0.7694 (mtpm) REVERT: 9 6 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.9048 (t80) REVERT: 9 7 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.7688 (ptmm) REVERT: 9 9 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7091 (OUTLIER) REVERT: 0 3 LYS cc_start: 0.7955 (mppt) cc_final: 0.7462 (mtpm) REVERT: 0 7 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7456 (ptpt) REVERT: AG 2 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8534 (m-10) REVERT: AA 3 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8056 (mtpm) REVERT: AA 7 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8688 (ttmm) REVERT: AB 7 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7107 (ptpp) REVERT: AN 7 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8860 (tttt) REVERT: AM 7 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.9001 (tptt) REVERT: AP 3 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7721 (ttmm) REVERT: AX 7 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8756 (mtpp) REVERT: AY 9 GLU cc_start: 0.8263 (mp0) cc_final: 0.7761 (mp0) REVERT: AU 7 LYS cc_start: 0.6675 (OUTLIER) cc_final: 0.5837 (tppt) REVERT: AT 9 GLU cc_start: 0.9313 (tt0) cc_final: 0.9088 (tt0) REVERT: Aa 7 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8542 (tptp) REVERT: Ad 7 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.7418 (tppt) outliers start: 84 outliers final: 36 residues processed: 170 average time/residue: 0.8835 time to fit residues: 153.9307 Evaluate side-chains 181 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 2 PHE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 7 LYS Chi-restraints excluded: chain b residue 4 PHE Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain X residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain R residue 9 GLU Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain m residue 2 PHE Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain n residue 4 PHE Chi-restraints excluded: chain n residue 6 PHE Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 9 GLU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain z residue 6 PHE Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain 1 residue 2 PHE Chi-restraints excluded: chain u residue 3 LYS Chi-restraints excluded: chain u residue 7 LYS Chi-restraints excluded: chain u residue 9 GLU Chi-restraints excluded: chain 2 residue 2 PHE Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 3 residue 7 LYS Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 4 residue 9 GLU Chi-restraints excluded: chain 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 6 PHE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain 0 residue 7 LYS Chi-restraints excluded: chain AG residue 2 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AA residue 2 PHE Chi-restraints excluded: chain AA residue 3 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AB residue 7 LYS Chi-restraints excluded: chain AE residue 9 GLU Chi-restraints excluded: chain AN residue 7 LYS Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AM residue 7 LYS Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AP residue 3 LYS Chi-restraints excluded: chain AW residue 6 PHE Chi-restraints excluded: chain AX residue 2 PHE Chi-restraints excluded: chain AX residue 7 LYS Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Chi-restraints excluded: chain Aa residue 7 LYS Chi-restraints excluded: chain Aa residue 9 GLU Chi-restraints excluded: chain Ad residue 7 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.085208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.065620 restraints weight = 14043.443| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.46 r_work: 0.2634 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.9240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.296 6150 Z= 3.167 Angle : 2.901 27.791 7800 Z= 1.446 Chirality : 0.162 0.528 525 Planarity : 0.014 0.116 975 Dihedral : 47.405 179.893 685 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 42.12 Ramachandran Plot: Outliers : 1.33 % Allowed : 39.78 % Favored : 58.89 % Rotamer: Outliers : 17.33 % Allowed : 25.33 % Favored : 57.33 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.48 (0.25), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.19), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.091 0.009 PHE n 6 Details of bonding type rmsd/Z covalent geometry : bond 0.07941 / 3.18 ( 6075) covalent geometry : angle 2.90072 / 1.45 ( 7800) hydrogen bonds : bond 0.08495 / 4.74 ( 158) hydrogen bonds : angle 5.78547 / 3.64 ( 474) Misc. bond : bond 0.01144 / 0.67 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 125 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8010 (mtpt) REVERT: M 7 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8457 (ttpp) REVERT: M 9 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8194 (mp0) REVERT: Z 2 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8283 (m-10) REVERT: b 3 LYS cc_start: 0.7966 (tmtt) cc_final: 0.7612 (tmtt) REVERT: b 4 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8693 (p90) REVERT: b 9 GLU cc_start: 0.8230 (mp0) cc_final: 0.7844 (mp0) REVERT: Q 9 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7668 (pm20) REVERT: k 3 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8334 (mtpp) REVERT: k 9 GLU cc_start: 0.7860 (mp0) cc_final: 0.7416 (mp0) REVERT: m 7 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8649 (mtpp) REVERT: T 3 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8041 (mptt) REVERT: j 3 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8887 (tttt) REVERT: o 7 LYS cc_start: 0.9074 (tttt) cc_final: 0.8762 (tttm) REVERT: z 9 GLU cc_start: 0.8578 (mp0) cc_final: 0.8135 (mp0) REVERT: t 3 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7740 (tppp) REVERT: t 7 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7465 (mptt) REVERT: 1 3 LYS cc_start: 0.7734 (tmtt) cc_final: 0.7122 (tmtt) REVERT: 2 2 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8841 (m-10) REVERT: 2 9 GLU cc_start: 0.8445 (mp0) cc_final: 0.8217 (mp0) REVERT: v 3 LYS cc_start: 0.8591 (mptt) cc_final: 0.8366 (mptt) REVERT: 3 7 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.7960 (mmtm) REVERT: 9 3 LYS cc_start: 0.8114 (tmtt) cc_final: 0.7664 (mtpm) REVERT: 9 6 PHE cc_start: 0.9349 (OUTLIER) cc_final: 0.9050 (t80) REVERT: 9 7 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8038 (ptmm) REVERT: 9 9 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: 0 3 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7550 (mtpm) REVERT: AA 2 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: AA 3 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8133 (mtpm) REVERT: AA 7 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8722 (ttmm) REVERT: AH 9 GLU cc_start: 0.8251 (mp0) cc_final: 0.7814 (mp0) REVERT: AB 7 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7381 (ptpp) REVERT: AN 7 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8757 (tttt) REVERT: AP 3 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7670 (ttmm) REVERT: AQ 2 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8901 (t80) REVERT: AY 9 GLU cc_start: 0.8310 (mp0) cc_final: 0.7812 (mp0) REVERT: AU 7 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.5866 (tppt) REVERT: Aa 7 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8530 (tptp) REVERT: Ad 7 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.7441 (tppt) outliers start: 91 outliers final: 39 residues processed: 178 average time/residue: 0.8227 time to fit residues: 150.2942 Evaluate side-chains 186 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 121 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 2 PHE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain Z residue 2 PHE Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain b residue 4 PHE Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain X residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain l residue 7 LYS Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain m residue 2 PHE Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain n residue 4 PHE Chi-restraints excluded: chain n residue 6 PHE Chi-restraints excluded: chain j residue 3 LYS Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 9 GLU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain q residue 9 GLU Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain U residue 2 PHE Chi-restraints excluded: chain z residue 6 PHE Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain 1 residue 2 PHE Chi-restraints excluded: chain u residue 3 LYS Chi-restraints excluded: chain u residue 7 LYS Chi-restraints excluded: chain 2 residue 2 PHE Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 3 residue 7 LYS Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 4 residue 9 GLU Chi-restraints excluded: chain 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 6 PHE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain 0 residue 3 LYS Chi-restraints excluded: chain 0 residue 7 LYS Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AA residue 2 PHE Chi-restraints excluded: chain AA residue 3 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AB residue 7 LYS Chi-restraints excluded: chain AE residue 9 GLU Chi-restraints excluded: chain AN residue 7 LYS Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 9 GLU Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AP residue 3 LYS Chi-restraints excluded: chain AW residue 6 PHE Chi-restraints excluded: chain AQ residue 2 PHE Chi-restraints excluded: chain AX residue 2 PHE Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Chi-restraints excluded: chain Aa residue 7 LYS Chi-restraints excluded: chain Aa residue 9 GLU Chi-restraints excluded: chain Ad residue 7 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.065826 restraints weight = 13113.307| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.37 r_work: 0.2638 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9138 moved from start: 0.9288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.290 6150 Z= 3.162 Angle : 2.895 28.350 7800 Z= 1.444 Chirality : 0.163 0.564 525 Planarity : 0.013 0.047 975 Dihedral : 47.294 179.871 685 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 41.07 Ramachandran Plot: Outliers : 1.56 % Allowed : 40.22 % Favored : 58.22 % Rotamer: Outliers : 17.90 % Allowed : 26.29 % Favored : 55.81 % Cbeta Deviations : 0.76 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.95 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.50 (0.26), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.95 (0.19), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.091 0.009 PHE n 6 Details of bonding type rmsd/Z covalent geometry : bond 0.07928 / 3.18 ( 6075) covalent geometry : angle 2.89514 / 1.44 ( 7800) hydrogen bonds : bond 0.08491 / 4.75 ( 158) hydrogen bonds : angle 5.80826 / 3.66 ( 474) Misc. bond : bond 0.01155 / 0.68 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 124 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8060 (mtpt) REVERT: M 7 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8591 (ttpp) REVERT: Z 2 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8303 (m-10) REVERT: b 3 LYS cc_start: 0.7967 (tmtt) cc_final: 0.7615 (tmtt) REVERT: b 4 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8674 (p90) REVERT: b 9 GLU cc_start: 0.8242 (mp0) cc_final: 0.7946 (mp0) REVERT: Q 9 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: k 3 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8341 (mtpp) REVERT: k 9 GLU cc_start: 0.7846 (mp0) cc_final: 0.7418 (mp0) REVERT: l 9 GLU cc_start: 0.8339 (mp0) cc_final: 0.7748 (mp0) REVERT: S 6 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.7822 (t80) REVERT: T 3 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8067 (mptt) REVERT: n 2 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: n 7 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8613 (mtmm) REVERT: o 7 LYS cc_start: 0.9063 (tttt) cc_final: 0.8755 (tttm) REVERT: z 9 GLU cc_start: 0.8584 (mp0) cc_final: 0.8165 (mp0) REVERT: t 3 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7620 (tppp) REVERT: t 7 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7616 (mptt) REVERT: 1 3 LYS cc_start: 0.7754 (tmtt) cc_final: 0.7154 (tmtt) REVERT: 2 2 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8842 (m-10) REVERT: 2 9 GLU cc_start: 0.8435 (mp0) cc_final: 0.8209 (mp0) REVERT: v 3 LYS cc_start: 0.8594 (mptt) cc_final: 0.8272 (mptt) REVERT: 3 7 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.7968 (mmtm) REVERT: 4 7 LYS cc_start: 0.9019 (tttt) cc_final: 0.8683 (tttm) REVERT: 9 3 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7657 (mtpm) REVERT: 9 6 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.9080 (t80) REVERT: 9 7 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8009 (ptmm) REVERT: 0 3 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7644 (mtpm) REVERT: AA 2 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: AA 3 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8103 (mtpm) REVERT: AA 7 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8739 (ttmm) REVERT: AH 9 GLU cc_start: 0.8255 (mp0) cc_final: 0.7781 (mp0) REVERT: AN 7 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8740 (tttt) REVERT: AP 3 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7631 (ttmm) REVERT: AQ 2 PHE cc_start: 0.9376 (OUTLIER) cc_final: 0.8985 (t80) REVERT: AQ 6 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.9067 (t80) REVERT: AY 9 GLU cc_start: 0.8301 (mp0) cc_final: 0.7753 (mp0) REVERT: AU 7 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.5845 (tppt) REVERT: Aa 7 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8538 (tptp) REVERT: Ad 7 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.7436 (tppt) outliers start: 94 outliers final: 45 residues processed: 181 average time/residue: 0.7886 time to fit residues: 146.4856 Evaluate side-chains 197 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 125 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 2 PHE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain Z residue 2 PHE Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain b residue 4 PHE Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain X residue 9 GLU Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain R residue 9 GLU Chi-restraints excluded: chain l residue 2 PHE Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain S residue 6 PHE Chi-restraints excluded: chain m residue 2 PHE Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain n residue 2 PHE Chi-restraints excluded: chain n residue 4 PHE Chi-restraints excluded: chain n residue 6 PHE Chi-restraints excluded: chain n residue 7 LYS Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 9 GLU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain q residue 9 GLU Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain z residue 6 PHE Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain 1 residue 2 PHE Chi-restraints excluded: chain u residue 3 LYS Chi-restraints excluded: chain u residue 6 PHE Chi-restraints excluded: chain 2 residue 2 PHE Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 3 residue 7 LYS Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 4 residue 9 GLU Chi-restraints excluded: chain 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 6 PHE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain 0 residue 3 LYS Chi-restraints excluded: chain 0 residue 7 LYS Chi-restraints excluded: chain AG residue 2 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AA residue 2 PHE Chi-restraints excluded: chain AA residue 3 LYS Chi-restraints excluded: chain AA residue 7 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AE residue 9 GLU Chi-restraints excluded: chain AN residue 7 LYS Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 9 GLU Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AO residue 9 GLU Chi-restraints excluded: chain AV residue 2 PHE Chi-restraints excluded: chain AP residue 3 LYS Chi-restraints excluded: chain AW residue 6 PHE Chi-restraints excluded: chain AQ residue 2 PHE Chi-restraints excluded: chain AQ residue 6 PHE Chi-restraints excluded: chain AX residue 2 PHE Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Chi-restraints excluded: chain Aa residue 7 LYS Chi-restraints excluded: chain Aa residue 9 GLU Chi-restraints excluded: chain Ad residue 7 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.065271 restraints weight = 14728.649| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 2.54 r_work: 0.2629 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 moved from start: 0.9356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.295 6150 Z= 3.159 Angle : 2.899 27.836 7800 Z= 1.445 Chirality : 0.163 0.573 525 Planarity : 0.013 0.047 975 Dihedral : 47.313 179.916 685 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 40.03 Ramachandran Plot: Outliers : 1.78 % Allowed : 40.89 % Favored : 57.33 % Rotamer: Outliers : 18.67 % Allowed : 25.90 % Favored : 55.43 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.50 (0.26), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.94 (0.19), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.092 0.009 PHE n 6 Details of bonding type rmsd/Z covalent geometry : bond 0.07920 / 3.18 ( 6075) covalent geometry : angle 2.89905 / 1.45 ( 7800) hydrogen bonds : bond 0.08499 / 4.74 ( 158) hydrogen bonds : angle 5.80606 / 3.66 ( 474) Misc. bond : bond 0.01150 / 0.67 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 126 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8075 (mtpt) REVERT: M 7 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8594 (ttpp) REVERT: Z 2 PHE cc_start: 0.9070 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: b 3 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7679 (tmtt) REVERT: b 4 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8661 (p90) REVERT: b 9 GLU cc_start: 0.8253 (mp0) cc_final: 0.7960 (mp0) REVERT: k 3 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8294 (mtpp) REVERT: k 9 GLU cc_start: 0.7837 (mp0) cc_final: 0.7412 (mp0) REVERT: l 9 GLU cc_start: 0.8352 (mp0) cc_final: 0.7666 (mp0) REVERT: S 6 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.7795 (t80) REVERT: T 3 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8055 (mptt) REVERT: n 2 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: n 7 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8602 (mtmm) REVERT: o 7 LYS cc_start: 0.9068 (tttt) cc_final: 0.8761 (tttm) REVERT: z 9 GLU cc_start: 0.8580 (mp0) cc_final: 0.8234 (mp0) REVERT: t 3 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7602 (tppp) REVERT: 1 3 LYS cc_start: 0.7718 (tmtt) cc_final: 0.7121 (tmtt) REVERT: u 7 LYS cc_start: 0.8761 (tmtp) cc_final: 0.8364 (tmtm) REVERT: 2 2 PHE cc_start: 0.9212 (OUTLIER) cc_final: 0.8837 (m-10) REVERT: 2 9 GLU cc_start: 0.8436 (mp0) cc_final: 0.8209 (mp0) REVERT: v 3 LYS cc_start: 0.8592 (mptt) cc_final: 0.8298 (mptt) REVERT: 9 3 LYS cc_start: 0.8119 (tmtt) cc_final: 0.7676 (mtpm) REVERT: 9 6 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.9068 (t80) REVERT: 9 7 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7978 (ptmm) REVERT: 0 3 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7650 (mmmm) REVERT: AA 2 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: AA 3 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8110 (mtpm) REVERT: AA 7 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8760 (ttmm) REVERT: AH 9 GLU cc_start: 0.8263 (mp0) cc_final: 0.7780 (mp0) REVERT: AN 7 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8793 (tttt) REVERT: AV 2 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8570 (m-10) REVERT: AP 3 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7623 (ttmm) REVERT: AQ 6 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.9063 (t80) REVERT: AR 7 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7505 (mmtt) REVERT: AY 9 GLU cc_start: 0.8332 (mp0) cc_final: 0.7772 (mp0) REVERT: AU 7 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.5877 (tppt) REVERT: Aa 7 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8547 (tptp) REVERT: Ad 7 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.7448 (tppt) outliers start: 98 outliers final: 49 residues processed: 188 average time/residue: 0.7574 time to fit residues: 146.3097 Evaluate side-chains 199 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 125 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 2 PHE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain Y residue 7 LYS Chi-restraints excluded: chain Z residue 2 PHE Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain b residue 4 PHE Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain X residue 9 GLU Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain R residue 9 GLU Chi-restraints excluded: chain l residue 2 PHE Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain S residue 6 PHE Chi-restraints excluded: chain m residue 2 PHE Chi-restraints excluded: chain m residue 4 PHE Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain n residue 2 PHE Chi-restraints excluded: chain n residue 4 PHE Chi-restraints excluded: chain n residue 6 PHE Chi-restraints excluded: chain n residue 7 LYS Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 9 GLU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain q residue 9 GLU Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain U residue 2 PHE Chi-restraints excluded: chain z residue 6 PHE Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain 1 residue 2 PHE Chi-restraints excluded: chain u residue 3 LYS Chi-restraints excluded: chain u residue 6 PHE Chi-restraints excluded: chain 2 residue 2 PHE Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 4 residue 9 GLU Chi-restraints excluded: chain 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 6 PHE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain 0 residue 2 PHE Chi-restraints excluded: chain 0 residue 3 LYS Chi-restraints excluded: chain 0 residue 7 LYS Chi-restraints excluded: chain AG residue 2 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AA residue 2 PHE Chi-restraints excluded: chain AA residue 3 LYS Chi-restraints excluded: chain AA residue 7 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AE residue 9 GLU Chi-restraints excluded: chain AN residue 7 LYS Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 9 GLU Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AV residue 2 PHE Chi-restraints excluded: chain AP residue 3 LYS Chi-restraints excluded: chain AW residue 6 PHE Chi-restraints excluded: chain AQ residue 6 PHE Chi-restraints excluded: chain AX residue 2 PHE Chi-restraints excluded: chain AR residue 7 LYS Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Chi-restraints excluded: chain Aa residue 7 LYS Chi-restraints excluded: chain Aa residue 9 GLU Chi-restraints excluded: chain Ad residue 7 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.085029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.065289 restraints weight = 14494.889| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 2.50 r_work: 0.2629 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 moved from start: 0.9372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.293 6150 Z= 3.159 Angle : 2.900 27.711 7800 Z= 1.447 Chirality : 0.163 0.580 525 Planarity : 0.013 0.047 975 Dihedral : 47.367 179.898 681 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 40.64 Ramachandran Plot: Outliers : 1.78 % Allowed : 40.89 % Favored : 57.33 % Rotamer: Outliers : 17.52 % Allowed : 27.43 % Favored : 55.05 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.47 (0.26), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.20), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.092 0.009 PHE n 6 Details of bonding type rmsd/Z covalent geometry : bond 0.07921 / 3.18 ( 6075) covalent geometry : angle 2.90040 / 1.45 ( 7800) hydrogen bonds : bond 0.08475 / 4.72 ( 158) hydrogen bonds : angle 5.80501 / 3.65 ( 474) Misc. bond : bond 0.01148 / 0.67 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 128 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8078 (mtpt) REVERT: M 7 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8605 (ttpp) REVERT: Z 2 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8219 (m-10) REVERT: b 3 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7676 (tmtt) REVERT: b 4 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8663 (p90) REVERT: b 9 GLU cc_start: 0.8246 (mp0) cc_final: 0.7949 (mp0) REVERT: k 3 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8289 (mtpp) REVERT: k 9 GLU cc_start: 0.7827 (mp0) cc_final: 0.7410 (mp0) REVERT: R 7 LYS cc_start: 0.8323 (mptt) cc_final: 0.7618 (mptt) REVERT: l 9 GLU cc_start: 0.8473 (mp0) cc_final: 0.7784 (mp0) REVERT: S 6 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.7757 (t80) REVERT: T 3 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8082 (mptt) REVERT: n 2 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8449 (m-80) REVERT: n 3 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7967 (tmtt) REVERT: n 7 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8604 (mtmm) REVERT: o 7 LYS cc_start: 0.9061 (tttt) cc_final: 0.8755 (tttm) REVERT: z 9 GLU cc_start: 0.8577 (mp0) cc_final: 0.8178 (mp0) REVERT: t 3 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7576 (tppp) REVERT: 1 3 LYS cc_start: 0.7733 (tmtt) cc_final: 0.7113 (tmtt) REVERT: u 7 LYS cc_start: 0.8751 (tmtp) cc_final: 0.8482 (tmtm) REVERT: 2 2 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8841 (m-10) REVERT: 2 9 GLU cc_start: 0.8437 (mp0) cc_final: 0.8211 (mp0) REVERT: v 3 LYS cc_start: 0.8595 (mptt) cc_final: 0.8303 (mptt) REVERT: 3 7 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8666 (mmtp) REVERT: 9 3 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7658 (mtpm) REVERT: 9 6 PHE cc_start: 0.9391 (OUTLIER) cc_final: 0.9076 (t80) REVERT: 9 7 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8018 (ptmm) REVERT: 0 3 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7589 (mmmm) REVERT: 0 7 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7579 (mptt) REVERT: AA 2 PHE cc_start: 0.9402 (OUTLIER) cc_final: 0.8556 (m-80) REVERT: AA 3 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8104 (mtpm) REVERT: AA 7 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8755 (ttmm) REVERT: AH 9 GLU cc_start: 0.8250 (mp0) cc_final: 0.7762 (mp0) REVERT: AN 7 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8765 (tttt) REVERT: AV 2 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8623 (m-10) REVERT: AP 3 LYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7638 (ttmm) REVERT: AQ 6 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.9061 (t80) REVERT: AY 9 GLU cc_start: 0.8335 (mp0) cc_final: 0.7779 (mp0) REVERT: AU 7 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5849 (tppt) REVERT: Aa 7 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8552 (tptp) REVERT: Ad 7 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.7440 (tppt) outliers start: 92 outliers final: 52 residues processed: 182 average time/residue: 0.7820 time to fit residues: 146.1619 Evaluate side-chains 205 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 127 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 2 PHE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain Z residue 2 PHE Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain b residue 2 PHE Chi-restraints excluded: chain b residue 4 PHE Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain X residue 9 GLU Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain R residue 9 GLU Chi-restraints excluded: chain l residue 2 PHE Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain S residue 6 PHE Chi-restraints excluded: chain m residue 2 PHE Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain n residue 2 PHE Chi-restraints excluded: chain n residue 4 PHE Chi-restraints excluded: chain n residue 6 PHE Chi-restraints excluded: chain n residue 7 LYS Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 9 GLU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain q residue 9 GLU Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain U residue 2 PHE Chi-restraints excluded: chain z residue 6 PHE Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain 1 residue 2 PHE Chi-restraints excluded: chain u residue 3 LYS Chi-restraints excluded: chain 2 residue 2 PHE Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 3 residue 7 LYS Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 4 residue 9 GLU Chi-restraints excluded: chain 6 residue 9 GLU Chi-restraints excluded: chain 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 6 PHE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain AF residue 2 PHE Chi-restraints excluded: chain 0 residue 2 PHE Chi-restraints excluded: chain 0 residue 3 LYS Chi-restraints excluded: chain 0 residue 7 LYS Chi-restraints excluded: chain AG residue 2 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AA residue 2 PHE Chi-restraints excluded: chain AA residue 3 LYS Chi-restraints excluded: chain AA residue 7 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AB residue 7 LYS Chi-restraints excluded: chain AE residue 9 GLU Chi-restraints excluded: chain AN residue 7 LYS Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 9 GLU Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AO residue 9 GLU Chi-restraints excluded: chain AV residue 2 PHE Chi-restraints excluded: chain AP residue 3 LYS Chi-restraints excluded: chain AW residue 2 PHE Chi-restraints excluded: chain AW residue 6 PHE Chi-restraints excluded: chain AQ residue 6 PHE Chi-restraints excluded: chain AX residue 2 PHE Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Chi-restraints excluded: chain Aa residue 7 LYS Chi-restraints excluded: chain Aa residue 9 GLU Chi-restraints excluded: chain Ad residue 7 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.065016 restraints weight = 15592.458| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.60 r_work: 0.2623 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.9401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.308 6150 Z= 3.158 Angle : 2.900 27.593 7800 Z= 1.448 Chirality : 0.163 0.584 525 Planarity : 0.013 0.047 975 Dihedral : 47.355 179.797 681 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 40.81 Ramachandran Plot: Outliers : 1.78 % Allowed : 41.11 % Favored : 57.11 % Rotamer: Outliers : 16.57 % Allowed : 28.95 % Favored : 54.48 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.48 (0.26), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.20), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.092 0.009 PHE n 6 Details of bonding type rmsd/Z covalent geometry : bond 0.07917 / 3.17 ( 6075) covalent geometry : angle 2.90048 / 1.45 ( 7800) hydrogen bonds : bond 0.08476 / 4.72 ( 158) hydrogen bonds : angle 5.81032 / 3.65 ( 474) Misc. bond : bond 0.01144 / 0.67 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 127 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8076 (mtpt) REVERT: M 7 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8591 (ttpp) REVERT: Z 2 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8220 (m-10) REVERT: Z 9 GLU cc_start: 0.8453 (mp0) cc_final: 0.8042 (mp0) REVERT: b 3 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7679 (tmtt) REVERT: b 4 PHE cc_start: 0.9303 (OUTLIER) cc_final: 0.8667 (p90) REVERT: b 9 GLU cc_start: 0.8253 (mp0) cc_final: 0.7977 (mp0) REVERT: k 3 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8321 (mtpp) REVERT: k 9 GLU cc_start: 0.7818 (mp0) cc_final: 0.7406 (mp0) REVERT: R 7 LYS cc_start: 0.8357 (mptt) cc_final: 0.7712 (mptt) REVERT: l 9 GLU cc_start: 0.8428 (mp0) cc_final: 0.7728 (mp0) REVERT: T 3 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8065 (mptt) REVERT: n 2 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: n 3 LYS cc_start: 0.8178 (tmtt) cc_final: 0.7949 (tmtt) REVERT: n 7 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8603 (mtmm) REVERT: o 7 LYS cc_start: 0.9064 (tttt) cc_final: 0.8754 (tttm) REVERT: z 9 GLU cc_start: 0.8582 (mp0) cc_final: 0.8201 (mp0) REVERT: t 3 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7697 (tppp) REVERT: 1 3 LYS cc_start: 0.7689 (tmtt) cc_final: 0.7098 (tmtt) REVERT: u 7 LYS cc_start: 0.8716 (tmtp) cc_final: 0.8485 (tmtm) REVERT: 2 2 PHE cc_start: 0.9220 (OUTLIER) cc_final: 0.8844 (m-10) REVERT: 2 9 GLU cc_start: 0.8435 (mp0) cc_final: 0.8205 (mp0) REVERT: v 3 LYS cc_start: 0.8599 (mptt) cc_final: 0.8313 (mptt) REVERT: 3 7 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8682 (mmtp) REVERT: 9 3 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7652 (mtpm) REVERT: 9 6 PHE cc_start: 0.9409 (OUTLIER) cc_final: 0.9097 (t80) REVERT: 9 7 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7892 (ptmm) REVERT: 0 3 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7573 (mmmm) REVERT: 0 7 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7743 (mptt) REVERT: AA 2 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: AA 3 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8111 (mtpm) REVERT: AA 7 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8764 (ttmm) REVERT: AH 9 GLU cc_start: 0.8255 (mp0) cc_final: 0.7770 (mp0) REVERT: AN 7 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8802 (tttt) REVERT: AV 2 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8605 (m-10) REVERT: AP 3 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7703 (ttmm) REVERT: AY 9 GLU cc_start: 0.8352 (mp0) cc_final: 0.7787 (mp0) REVERT: AU 7 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.5858 (tppt) REVERT: Aa 7 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8551 (tptp) REVERT: Ad 7 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.7441 (tppt) outliers start: 87 outliers final: 51 residues processed: 179 average time/residue: 0.8448 time to fit residues: 155.0759 Evaluate side-chains 201 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 126 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 2 PHE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain Z residue 2 PHE Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain b residue 2 PHE Chi-restraints excluded: chain b residue 4 PHE Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain X residue 9 GLU Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain l residue 2 PHE Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain m residue 2 PHE Chi-restraints excluded: chain m residue 4 PHE Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain n residue 2 PHE Chi-restraints excluded: chain n residue 4 PHE Chi-restraints excluded: chain n residue 6 PHE Chi-restraints excluded: chain n residue 7 LYS Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 9 GLU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain q residue 9 GLU Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain U residue 2 PHE Chi-restraints excluded: chain z residue 6 PHE Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain 1 residue 2 PHE Chi-restraints excluded: chain u residue 3 LYS Chi-restraints excluded: chain 2 residue 2 PHE Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 3 residue 7 LYS Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 4 residue 9 GLU Chi-restraints excluded: chain 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 6 PHE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain AF residue 2 PHE Chi-restraints excluded: chain 0 residue 2 PHE Chi-restraints excluded: chain 0 residue 3 LYS Chi-restraints excluded: chain 0 residue 7 LYS Chi-restraints excluded: chain AG residue 2 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AA residue 2 PHE Chi-restraints excluded: chain AA residue 3 LYS Chi-restraints excluded: chain AA residue 7 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AB residue 7 LYS Chi-restraints excluded: chain AE residue 9 GLU Chi-restraints excluded: chain AN residue 7 LYS Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 9 GLU Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AO residue 9 GLU Chi-restraints excluded: chain AV residue 2 PHE Chi-restraints excluded: chain AP residue 3 LYS Chi-restraints excluded: chain AW residue 2 PHE Chi-restraints excluded: chain AW residue 6 PHE Chi-restraints excluded: chain AX residue 2 PHE Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Chi-restraints excluded: chain Aa residue 7 LYS Chi-restraints excluded: chain Aa residue 9 GLU Chi-restraints excluded: chain Ad residue 7 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.065348 restraints weight = 14732.655| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.51 r_work: 0.2628 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.9388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.308 6150 Z= 3.157 Angle : 2.903 27.516 7800 Z= 1.450 Chirality : 0.163 0.585 525 Planarity : 0.013 0.046 975 Dihedral : 47.356 179.827 681 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 41.07 Ramachandran Plot: Outliers : 1.78 % Allowed : 41.33 % Favored : 56.89 % Rotamer: Outliers : 15.81 % Allowed : 29.71 % Favored : 54.48 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.47 (0.26), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.20), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.092 0.009 PHE n 6 Details of bonding type rmsd/Z covalent geometry : bond 0.07917 / 3.17 ( 6075) covalent geometry : angle 2.90317 / 1.45 ( 7800) hydrogen bonds : bond 0.08481 / 4.71 ( 158) hydrogen bonds : angle 5.82398 / 3.66 ( 474) Misc. bond : bond 0.01145 / 0.67 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 129 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 3 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8070 (mtpt) REVERT: M 7 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8593 (ttpp) REVERT: Z 2 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8215 (m-10) REVERT: b 3 LYS cc_start: 0.8025 (tmtt) cc_final: 0.7682 (tmtt) REVERT: b 4 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8667 (p90) REVERT: b 9 GLU cc_start: 0.8249 (mp0) cc_final: 0.7973 (mp0) REVERT: k 3 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8318 (mtpp) REVERT: k 9 GLU cc_start: 0.7822 (mp0) cc_final: 0.7413 (mp0) REVERT: R 7 LYS cc_start: 0.8368 (mptt) cc_final: 0.7711 (mptt) REVERT: l 9 GLU cc_start: 0.8442 (mp0) cc_final: 0.7765 (mp0) REVERT: T 3 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8064 (mptt) REVERT: n 2 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: n 3 LYS cc_start: 0.8180 (tmtt) cc_final: 0.7944 (tmtt) REVERT: n 7 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8604 (mtmm) REVERT: o 7 LYS cc_start: 0.9062 (tttt) cc_final: 0.8761 (tttm) REVERT: z 9 GLU cc_start: 0.8577 (mp0) cc_final: 0.8246 (mp0) REVERT: t 3 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7714 (tppp) REVERT: 1 3 LYS cc_start: 0.7691 (tmtt) cc_final: 0.7108 (tmtt) REVERT: u 7 LYS cc_start: 0.8740 (tmtp) cc_final: 0.8346 (tmtm) REVERT: 2 2 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8844 (m-10) REVERT: 2 9 GLU cc_start: 0.8431 (mp0) cc_final: 0.8204 (mp0) REVERT: v 3 LYS cc_start: 0.8602 (mptt) cc_final: 0.8320 (mptt) REVERT: 3 7 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8670 (mmtp) REVERT: 9 3 LYS cc_start: 0.8104 (tmtt) cc_final: 0.7660 (mtpm) REVERT: 9 6 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.9098 (t80) REVERT: 9 7 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7915 (ptmm) REVERT: 0 3 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7570 (mmmm) REVERT: AA 2 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.8555 (m-80) REVERT: AA 3 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8111 (mtpm) REVERT: AA 7 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8756 (ttmm) REVERT: AH 9 GLU cc_start: 0.8248 (mp0) cc_final: 0.7761 (mp0) REVERT: AN 7 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8798 (tttt) REVERT: AV 2 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8606 (m-10) REVERT: AW 3 LYS cc_start: 0.8331 (tptt) cc_final: 0.8030 (tptt) REVERT: AY 9 GLU cc_start: 0.8371 (mp0) cc_final: 0.7789 (mp0) REVERT: AU 7 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.5844 (tppt) REVERT: Aa 7 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8554 (tptp) REVERT: Ad 7 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.7423 (tppt) outliers start: 83 outliers final: 52 residues processed: 176 average time/residue: 0.7707 time to fit residues: 139.2860 Evaluate side-chains 203 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 129 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 2 PHE Chi-restraints excluded: chain M residue 3 LYS Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain M residue 9 GLU Chi-restraints excluded: chain Z residue 2 PHE Chi-restraints excluded: chain Z residue 7 LYS Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain b residue 2 PHE Chi-restraints excluded: chain b residue 4 PHE Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain X residue 9 GLU Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain k residue 3 LYS Chi-restraints excluded: chain R residue 9 GLU Chi-restraints excluded: chain l residue 2 PHE Chi-restraints excluded: chain S residue 2 PHE Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain m residue 2 PHE Chi-restraints excluded: chain m residue 4 PHE Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain n residue 2 PHE Chi-restraints excluded: chain n residue 4 PHE Chi-restraints excluded: chain n residue 6 PHE Chi-restraints excluded: chain n residue 7 LYS Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain p residue 7 LYS Chi-restraints excluded: chain p residue 9 GLU Chi-restraints excluded: chain s residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain q residue 9 GLU Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain U residue 2 PHE Chi-restraints excluded: chain z residue 6 PHE Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain 1 residue 2 PHE Chi-restraints excluded: chain u residue 3 LYS Chi-restraints excluded: chain 2 residue 2 PHE Chi-restraints excluded: chain 2 residue 7 LYS Chi-restraints excluded: chain 3 residue 7 LYS Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 4 residue 9 GLU Chi-restraints excluded: chain 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 6 PHE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 9 residue 9 GLU Chi-restraints excluded: chain AF residue 2 PHE Chi-restraints excluded: chain 0 residue 2 PHE Chi-restraints excluded: chain 0 residue 3 LYS Chi-restraints excluded: chain AG residue 2 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AA residue 2 PHE Chi-restraints excluded: chain AA residue 3 LYS Chi-restraints excluded: chain AA residue 7 LYS Chi-restraints excluded: chain AH residue 2 PHE Chi-restraints excluded: chain AB residue 7 LYS Chi-restraints excluded: chain AE residue 9 GLU Chi-restraints excluded: chain AN residue 7 LYS Chi-restraints excluded: chain AJ residue 7 LYS Chi-restraints excluded: chain AJ residue 9 GLU Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AO residue 9 GLU Chi-restraints excluded: chain AV residue 2 PHE Chi-restraints excluded: chain AW residue 2 PHE Chi-restraints excluded: chain AW residue 6 PHE Chi-restraints excluded: chain AX residue 2 PHE Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Chi-restraints excluded: chain Aa residue 7 LYS Chi-restraints excluded: chain Aa residue 9 GLU Chi-restraints excluded: chain Ad residue 7 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.065266 restraints weight = 15016.951| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.55 r_work: 0.2627 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.9406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.079 0.310 6150 Z= 3.157 Angle : 2.906 27.438 7800 Z= 1.451 Chirality : 0.164 0.586 525 Planarity : 0.013 0.046 975 Dihedral : 47.398 179.863 677 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 41.07 Ramachandran Plot: Outliers : 1.78 % Allowed : 41.56 % Favored : 56.67 % Rotamer: Outliers : 15.24 % Allowed : 30.67 % Favored : 54.10 % Cbeta Deviations : 0.95 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.47 (0.26), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.93 (0.20), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.092 0.009 PHE n 6 Details of bonding type rmsd/Z covalent geometry : bond 0.07918 / 3.17 ( 6075) covalent geometry : angle 2.90609 / 1.45 ( 7800) hydrogen bonds : bond 0.08483 / 4.71 ( 158) hydrogen bonds : angle 5.82223 / 3.66 ( 474) Misc. bond : bond 0.01144 / 0.67 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2337.25 seconds wall clock time: 40 minutes 22.32 seconds (2422.32 seconds total)