Starting phenix.real_space_refine on Thu Oct 22 21:29:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pdw_71546/10_2026/9pdw_71546.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pdw_71546/10_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_71546/10_2026/9pdw_71546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pdw_71546/10_2026/9pdw_71546.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pdw_71546/10_2026/9pdw_71546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pdw_71546/10_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-2.3rc1-6221/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: 1.24, per 1000 atoms: 0.21 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: 0.48 Conformation dependent library (CDL) restraints added in 133.4 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: 0.15 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: 0.69 Time building geometry restraints manager: 0.64 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: 0.530 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.090 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- 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 : 0.156 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: 0.6122 time to fit residues: 89.7946 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 : 0.218 ------------------------------------------------------------------------------- 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: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.148659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.127913 restraints weight = 8376.383| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.68 r_work: 0.3635 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6150 Z= 0.137 Angle : 0.648 5.452 7800 Z= 0.315 Chirality : 0.031 0.087 525 Planarity : 0.003 0.012 975 Dihedral : 52.859 179.944 702 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 6.67 % Allowed : 34.86 % Favored : 58.48 % 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: -3.48 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE T 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6075) covalent geometry : angle 0.64802 / 0.31 ( 7800) hydrogen bonds : bond 0.03054 / 1.73 ( 158) hydrogen bonds : angle 4.50328 / 2.93 ( 474) Misc. bond : bond 0.00042 / 0.02 ( 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 146 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.155 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: Y 3 LYS cc_start: 0.6693 (OUTLIER) cc_final: 0.6485 (tmtt) REVERT: Z 7 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7788 (mmtm) REVERT: Q 9 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.5525 (pm20) REVERT: k 7 LYS cc_start: 0.7608 (mmtt) cc_final: 0.6980 (ttmm) REVERT: R 3 LYS cc_start: 0.7261 (mppt) cc_final: 0.6956 (ttpp) REVERT: z 7 LYS cc_start: 0.7849 (ttmm) cc_final: 0.7592 (ttmm) REVERT: u 7 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7456 (tmtp) REVERT: 3 9 GLU cc_start: 0.7810 (mp0) cc_final: 0.7557 (mp0) REVERT: 9 3 LYS cc_start: 0.7018 (tmtt) cc_final: 0.6617 (tmtt) REVERT: AA 7 LYS cc_start: 0.7537 (mtpm) cc_final: 0.7295 (ptmt) REVERT: AI 2 PHE cc_start: 0.5159 (OUTLIER) cc_final: 0.4940 (OUTLIER) REVERT: AI 9 GLU cc_start: 0.7696 (mp0) cc_final: 0.7195 (mp0) REVERT: AR 7 LYS cc_start: 0.7496 (mmtt) cc_final: 0.7018 (mmtt) REVERT: AY 9 GLU cc_start: 0.7571 (mp0) cc_final: 0.7242 (mp0) REVERT: AU 7 LYS cc_start: 0.4220 (OUTLIER) cc_final: 0.3243 (ttpp) REVERT: Ad 7 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7194 (pttt) outliers start: 35 outliers final: 7 residues processed: 136 average time/residue: 0.7735 time to fit residues: 108.5024 Evaluate side-chains 113 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 3 LYS Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain n residue 2 PHE Chi-restraints excluded: chain n residue 7 LYS Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain u residue 7 LYS Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain AB residue 7 LYS Chi-restraints excluded: chain AI residue 2 PHE Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain Ad residue 7 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.118041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.095555 restraints weight = 8140.735| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.49 r_work: 0.3177 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.090 6150 Z= 0.683 Angle : 1.110 10.029 7800 Z= 0.544 Chirality : 0.044 0.176 525 Planarity : 0.005 0.021 975 Dihedral : 53.365 179.907 681 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 22.00 % Favored : 77.78 % Rotamer: Outliers : 8.95 % Allowed : 29.52 % Favored : 61.52 % 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: -3.61 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.029 0.004 PHE m 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01729 / 0.69 ( 6075) covalent geometry : angle 1.10974 / 0.54 ( 7800) hydrogen bonds : bond 0.04336 / 2.51 ( 158) hydrogen bonds : angle 4.31964 / 2.76 ( 474) Misc. bond : bond 0.00190 / 0.11 ( 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 122 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 7 LYS cc_start: 0.8780 (OUTLIER) cc_final: 0.8429 (ttpp) REVERT: b 7 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7972 (mtmm) REVERT: g 9 GLU cc_start: 0.8924 (mt-10) cc_final: 0.6962 (pm20) REVERT: Q 9 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: R 3 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7353 (ttmm) REVERT: T 3 LYS cc_start: 0.8582 (mtmm) cc_final: 0.7960 (mtpm) REVERT: 1 7 LYS cc_start: 0.8180 (mttp) cc_final: 0.7256 (mmtm) REVERT: v 3 LYS cc_start: 0.8301 (mptt) cc_final: 0.7498 (mtpm) REVERT: 8 9 GLU cc_start: 0.8932 (tt0) cc_final: 0.8542 (tt0) REVERT: 9 3 LYS cc_start: 0.7485 (tmtt) cc_final: 0.7189 (tmtt) REVERT: AG 6 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7543 (p90) REVERT: AG 7 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7314 (mmtm) REVERT: AA 4 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8548 (t80) REVERT: AA 7 LYS cc_start: 0.8389 (mtpm) cc_final: 0.8171 (ttmm) REVERT: AN 9 GLU cc_start: 0.8981 (tt0) cc_final: 0.8664 (tt0) REVERT: AM 9 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8561 (pp20) REVERT: AV 7 LYS cc_start: 0.8590 (mmtm) cc_final: 0.8309 (mttm) REVERT: AP 3 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6654 (ttpt) REVERT: AW 7 LYS cc_start: 0.8495 (mttm) cc_final: 0.7704 (mmtm) REVERT: AQ 7 LYS cc_start: 0.8516 (mtpm) cc_final: 0.8040 (ttmm) REVERT: AX 9 GLU cc_start: 0.8326 (mp0) cc_final: 0.8117 (mp0) REVERT: AY 9 GLU cc_start: 0.8013 (mp0) cc_final: 0.7772 (mp0) REVERT: AS 9 GLU cc_start: 0.8993 (tt0) cc_final: 0.8599 (tt0) REVERT: AU 3 LYS cc_start: 0.8524 (ptmt) cc_final: 0.6330 (tptt) REVERT: AU 7 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.4058 (tttm) REVERT: Ad 7 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.7089 (tppt) REVERT: Ad 9 GLU cc_start: 0.8815 (tt0) cc_final: 0.8426 (tt0) outliers start: 47 outliers final: 10 residues processed: 102 average time/residue: 0.9351 time to fit residues: 98.0357 Evaluate side-chains 95 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 7 LYS Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain R residue 3 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 7 residue 9 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain AG residue 6 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AA residue 4 PHE Chi-restraints excluded: chain AI residue 2 PHE 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 AY residue 2 PHE Chi-restraints excluded: chain AU residue 7 LYS Chi-restraints excluded: chain Ad residue 7 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.132857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.110255 restraints weight = 7992.946| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.61 r_work: 0.3354 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6150 Z= 0.118 Angle : 0.631 7.725 7800 Z= 0.306 Chirality : 0.030 0.077 525 Planarity : 0.002 0.009 975 Dihedral : 53.554 180.000 681 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.95 % Allowed : 32.19 % Favored : 62.86 % 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: -3.56 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHEAH 4 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 6075) covalent geometry : angle 0.63063 / 0.31 ( 7800) hydrogen bonds : bond 0.03253 / 1.82 ( 158) hydrogen bonds : angle 4.13499 / 2.69 ( 474) Misc. bond : bond 0.00032 / 0.02 ( 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 107 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 3 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.6891 (ttpp) REVERT: T 3 LYS cc_start: 0.8493 (mtmm) cc_final: 0.7905 (mtpm) REVERT: 1 7 LYS cc_start: 0.8203 (mttp) cc_final: 0.7523 (mmtm) REVERT: v 3 LYS cc_start: 0.8232 (mptt) cc_final: 0.7480 (mtpm) REVERT: v 7 LYS cc_start: 0.7926 (mptt) cc_final: 0.7687 (mptt) REVERT: 3 9 GLU cc_start: 0.7856 (mp0) cc_final: 0.7511 (mp0) REVERT: 8 9 GLU cc_start: 0.8620 (tt0) cc_final: 0.8265 (tt0) REVERT: 9 3 LYS cc_start: 0.7565 (tmtt) cc_final: 0.7175 (tmtt) REVERT: 0 3 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6955 (ttpp) REVERT: AG 7 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7512 (mmtm) REVERT: AB 3 LYS cc_start: 0.8412 (mppt) cc_final: 0.8212 (mptt) REVERT: AI 9 GLU cc_start: 0.7866 (mp0) cc_final: 0.7551 (mp0) REVERT: AL 3 LYS cc_start: 0.8685 (tttt) cc_final: 0.8440 (tttp) REVERT: AR 3 LYS cc_start: 0.8226 (mptt) cc_final: 0.7939 (mppt) REVERT: AR 7 LYS cc_start: 0.7837 (mptt) cc_final: 0.7580 (mptt) REVERT: AY 9 GLU cc_start: 0.7970 (mp0) cc_final: 0.7662 (mp0) REVERT: AS 9 GLU cc_start: 0.8650 (tt0) cc_final: 0.8309 (tt0) REVERT: AU 3 LYS cc_start: 0.8298 (ptmt) cc_final: 0.5967 (tptt) REVERT: Ad 7 LYS cc_start: 0.8453 (ptmt) cc_final: 0.6639 (tppt) REVERT: Ad 9 GLU cc_start: 0.8681 (tt0) cc_final: 0.8129 (tt0) outliers start: 26 outliers final: 9 residues processed: 96 average time/residue: 0.9523 time to fit residues: 93.9670 Evaluate side-chains 91 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain R residue 3 LYS Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain 1 residue 6 PHE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain 0 residue 3 LYS Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AK residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AU residue 9 GLU Chi-restraints excluded: chain Aa residue 9 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.116419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094714 restraints weight = 8968.790| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.65 r_work: 0.3085 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.7228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.060 6150 Z= 0.594 Angle : 0.946 8.749 7800 Z= 0.461 Chirality : 0.038 0.116 525 Planarity : 0.004 0.017 975 Dihedral : 53.251 179.984 679 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.44 % Favored : 75.56 % Rotamer: Outliers : 6.86 % Allowed : 30.10 % Favored : 63.05 % 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: -3.90 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.003 PHE m 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01496 / 0.60 ( 6075) covalent geometry : angle 0.94610 / 0.46 ( 7800) hydrogen bonds : bond 0.04023 / 2.31 ( 158) hydrogen bonds : angle 3.93398 / 2.49 ( 474) Misc. bond : bond 0.00229 / 0.14 ( 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 104 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.229 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: g 9 GLU cc_start: 0.8800 (mt-10) cc_final: 0.6755 (pm20) REVERT: R 3 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.6751 (ttpp) REVERT: m 7 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7611 (mptt) REVERT: T 3 LYS cc_start: 0.8486 (mtmm) cc_final: 0.7884 (mtpm) REVERT: 1 7 LYS cc_start: 0.8239 (mttp) cc_final: 0.7455 (mmtm) REVERT: v 3 LYS cc_start: 0.8360 (mptt) cc_final: 0.7551 (mtpm) REVERT: 3 9 GLU cc_start: 0.8070 (mp0) cc_final: 0.7497 (mp0) REVERT: 8 9 GLU cc_start: 0.8973 (tt0) cc_final: 0.8596 (tt0) REVERT: AG 6 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8051 (p90) REVERT: AG 7 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7800 (mptt) REVERT: AA 3 LYS cc_start: 0.8053 (mtpm) cc_final: 0.7776 (mtpt) REVERT: AB 3 LYS cc_start: 0.8488 (mppt) cc_final: 0.8216 (mptt) REVERT: AI 9 GLU cc_start: 0.8178 (mp0) cc_final: 0.7925 (mp0) REVERT: AV 7 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8308 (mttm) REVERT: AR 3 LYS cc_start: 0.8292 (mptt) cc_final: 0.8041 (mmtt) REVERT: AY 9 GLU cc_start: 0.8144 (mp0) cc_final: 0.7850 (mp0) REVERT: AS 9 GLU cc_start: 0.8883 (tt0) cc_final: 0.8393 (tt0) REVERT: AU 3 LYS cc_start: 0.8554 (ptmt) cc_final: 0.6232 (tptt) REVERT: AU 7 LYS cc_start: 0.6436 (OUTLIER) cc_final: 0.5976 (tptt) REVERT: Ad 7 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7030 (tppt) REVERT: Ad 9 GLU cc_start: 0.8932 (tt0) cc_final: 0.8678 (tt0) outliers start: 36 outliers final: 18 residues processed: 87 average time/residue: 0.9716 time to fit residues: 86.9073 Evaluate side-chains 93 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain d residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain R residue 3 LYS Chi-restraints excluded: chain m residue 7 LYS Chi-restraints excluded: chain j residue 9 GLU Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain r residue 9 GLU Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain 1 residue 6 PHE Chi-restraints excluded: chain 3 residue 2 PHE 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 AG residue 6 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AI residue 2 PHE Chi-restraints excluded: chain AM residue 9 GLU Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AV 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 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: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.128106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.105911 restraints weight = 8522.613| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.72 r_work: 0.3266 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6150 Z= 0.110 Angle : 0.626 7.623 7800 Z= 0.304 Chirality : 0.029 0.073 525 Planarity : 0.002 0.014 975 Dihedral : 53.486 179.978 679 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 5.14 % Allowed : 32.19 % Favored : 62.67 % 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: -3.64 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHEAH 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6075) covalent geometry : angle 0.62581 / 0.30 ( 7800) hydrogen bonds : bond 0.02966 / 1.65 ( 158) hydrogen bonds : angle 3.89619 / 2.51 ( 474) Misc. bond : bond 0.00030 / 0.02 ( 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 105 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 9 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8257 (mt-10) REVERT: Q 9 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.5779 (mp0) REVERT: R 3 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6872 (ttpp) REVERT: R 7 LYS cc_start: 0.7880 (mttp) cc_final: 0.7676 (mptp) REVERT: m 7 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7319 (mptt) REVERT: T 3 LYS cc_start: 0.8390 (mtmm) cc_final: 0.7773 (mtpm) REVERT: U 3 LYS cc_start: 0.7384 (tmtt) cc_final: 0.7114 (ttpt) REVERT: 1 7 LYS cc_start: 0.8129 (mttp) cc_final: 0.7376 (mmtm) REVERT: v 3 LYS cc_start: 0.8195 (mptt) cc_final: 0.7386 (mtpm) REVERT: 3 9 GLU cc_start: 0.7978 (mp0) cc_final: 0.7530 (mp0) REVERT: 8 9 GLU cc_start: 0.8715 (tt0) cc_final: 0.8281 (tt0) REVERT: AG 7 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7296 (mmtm) REVERT: AA 3 LYS cc_start: 0.7920 (mtpm) cc_final: 0.7633 (mtpt) REVERT: AA 7 LYS cc_start: 0.7948 (mtpm) cc_final: 0.7124 (mmtt) REVERT: AI 9 GLU cc_start: 0.8029 (mp0) cc_final: 0.7703 (mp0) REVERT: AL 3 LYS cc_start: 0.8734 (tttt) cc_final: 0.8521 (tttp) REVERT: AR 3 LYS cc_start: 0.8182 (mptt) cc_final: 0.7891 (mppt) REVERT: AY 9 GLU cc_start: 0.8064 (mp0) cc_final: 0.7728 (mp0) REVERT: AS 9 GLU cc_start: 0.8476 (tt0) cc_final: 0.8037 (tt0) REVERT: AU 3 LYS cc_start: 0.8304 (ptmt) cc_final: 0.5918 (tptt) REVERT: Ad 7 LYS cc_start: 0.8512 (ptmt) cc_final: 0.6681 (tppt) REVERT: Ad 9 GLU cc_start: 0.8681 (tt0) cc_final: 0.8315 (tt0) outliers start: 27 outliers final: 7 residues processed: 90 average time/residue: 0.9734 time to fit residues: 89.9407 Evaluate side-chains 85 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 9 GLU Chi-restraints excluded: chain Q residue 9 GLU Chi-restraints excluded: chain R residue 3 LYS Chi-restraints excluded: chain m residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain 1 residue 6 PHE Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AO residue 7 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.115335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093356 restraints weight = 9318.067| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.67 r_work: 0.3061 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.057 6150 Z= 0.584 Angle : 0.963 8.628 7800 Z= 0.464 Chirality : 0.038 0.106 525 Planarity : 0.004 0.016 975 Dihedral : 53.301 179.993 679 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.00 % Favored : 76.00 % Rotamer: Outliers : 7.81 % Allowed : 30.48 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they 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 : -3.03 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.026 0.003 PHE m 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01469 / 0.59 ( 6075) covalent geometry : angle 0.96328 / 0.46 ( 7800) hydrogen bonds : bond 0.03960 / 2.26 ( 158) hydrogen bonds : angle 3.86412 / 2.42 ( 474) Misc. bond : bond 0.00230 / 0.14 ( 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 107 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 66 time to evaluate : 0.229 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: R 3 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7133 (mtpp) REVERT: l 3 LYS cc_start: 0.7248 (tmtt) cc_final: 0.6871 (tmtt) REVERT: m 7 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7501 (mptt) REVERT: T 3 LYS cc_start: 0.8395 (mtmm) cc_final: 0.7788 (mtpm) REVERT: U 3 LYS cc_start: 0.7415 (tmtt) cc_final: 0.7207 (tttm) REVERT: t 3 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7067 (ttpp) REVERT: v 3 LYS cc_start: 0.8297 (mptt) cc_final: 0.7506 (mtpm) REVERT: 3 9 GLU cc_start: 0.8068 (mp0) cc_final: 0.7425 (mp0) REVERT: 8 9 GLU cc_start: 0.9008 (tt0) cc_final: 0.8659 (tt0) REVERT: AG 6 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7460 (p90) REVERT: AG 7 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7164 (mmtm) REVERT: AI 9 GLU cc_start: 0.8129 (mp0) cc_final: 0.7862 (mp0) REVERT: AV 7 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8308 (mttm) REVERT: AP 3 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.6884 (ttpt) REVERT: AY 9 GLU cc_start: 0.8106 (mp0) cc_final: 0.7805 (mp0) REVERT: AU 7 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.4067 (tttm) REVERT: Ad 7 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.6979 (tppt) REVERT: Ad 9 GLU cc_start: 0.8854 (tt0) cc_final: 0.8611 (tt0) outliers start: 41 outliers final: 16 residues processed: 90 average time/residue: 0.9336 time to fit residues: 86.3547 Evaluate side-chains 88 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain d residue 9 GLU Chi-restraints excluded: chain c residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain R residue 3 LYS Chi-restraints excluded: chain m residue 7 LYS Chi-restraints excluded: chain j residue 9 GLU 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 6 PHE Chi-restraints excluded: chain y residue 9 GLU Chi-restraints excluded: chain 4 residue 9 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain AG residue 6 PHE Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AO residue 7 LYS Chi-restraints excluded: chain AV residue 7 LYS Chi-restraints excluded: chain AP residue 3 LYS Chi-restraints excluded: chain AY residue 2 PHE Chi-restraints excluded: chain AU 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: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.126236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.104115 restraints weight = 8410.192| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.69 r_work: 0.3232 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.7514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6150 Z= 0.120 Angle : 0.681 8.024 7800 Z= 0.328 Chirality : 0.028 0.070 525 Planarity : 0.002 0.013 975 Dihedral : 53.522 179.998 679 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 4.19 % Allowed : 33.71 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHEAH 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 6075) covalent geometry : angle 0.68063 / 0.33 ( 7800) hydrogen bonds : bond 0.03191 / 1.79 ( 158) hydrogen bonds : angle 3.83142 / 2.48 ( 474) Misc. bond : bond 0.00031 / 0.02 ( 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 94 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.215 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: m 7 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7389 (mptt) REVERT: T 3 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7775 (mtpm) REVERT: U 3 LYS cc_start: 0.7486 (tmtt) cc_final: 0.7159 (ttpt) REVERT: v 3 LYS cc_start: 0.8216 (mptt) cc_final: 0.7434 (mtpm) REVERT: 3 9 GLU cc_start: 0.8049 (mp0) cc_final: 0.7530 (mp0) REVERT: 8 9 GLU cc_start: 0.8817 (tt0) cc_final: 0.8425 (tt0) REVERT: AG 7 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7253 (mmtm) REVERT: AA 3 LYS cc_start: 0.7849 (mtpm) cc_final: 0.7064 (tmtt) REVERT: AA 7 LYS cc_start: 0.7967 (mtpm) cc_final: 0.7154 (mmtt) REVERT: AB 3 LYS cc_start: 0.8311 (mptt) cc_final: 0.7922 (mppt) REVERT: AI 9 GLU cc_start: 0.8065 (mp0) cc_final: 0.7742 (mp0) REVERT: AD 9 GLU cc_start: 0.8858 (tt0) cc_final: 0.8519 (tm-30) REVERT: AL 3 LYS cc_start: 0.8758 (tttt) cc_final: 0.8538 (tttp) REVERT: AP 7 LYS cc_start: 0.7650 (mttp) cc_final: 0.7263 (mptp) REVERT: AR 3 LYS cc_start: 0.8165 (mptt) cc_final: 0.7941 (mppt) REVERT: AY 9 GLU cc_start: 0.8110 (mp0) cc_final: 0.7714 (mp0) REVERT: AS 9 GLU cc_start: 0.8709 (tt0) cc_final: 0.8498 (tt0) REVERT: AU 3 LYS cc_start: 0.8345 (ptmt) cc_final: 0.6001 (tptt) REVERT: Ad 7 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.6819 (tppt) REVERT: Ad 9 GLU cc_start: 0.8500 (tt0) cc_final: 0.8147 (tt0) outliers start: 22 outliers final: 10 residues processed: 82 average time/residue: 0.9550 time to fit residues: 80.4071 Evaluate side-chains 84 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain d residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain R residue 3 LYS Chi-restraints excluded: chain m residue 7 LYS Chi-restraints excluded: chain o residue 9 GLU Chi-restraints excluded: chain z residue 6 PHE Chi-restraints excluded: chain t residue 3 LYS Chi-restraints excluded: chain 4 residue 9 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain AG residue 7 LYS Chi-restraints excluded: chain AO residue 7 LYS 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: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.112048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.090907 restraints weight = 8786.267| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.52 r_work: 0.3066 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.054 6150 Z= 0.576 Angle : 0.981 9.516 7800 Z= 0.474 Chirality : 0.039 0.130 525 Planarity : 0.004 0.017 975 Dihedral : 53.391 179.969 675 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.00 % Favored : 76.00 % Rotamer: Outliers : 5.14 % Allowed : 32.38 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.23), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.003 PHEAV 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01454 / 0.58 ( 6075) covalent geometry : angle 0.98137 / 0.47 ( 7800) hydrogen bonds : bond 0.03865 / 2.23 ( 158) hydrogen bonds : angle 3.80560 / 2.40 ( 474) Misc. bond : bond 0.00233 / 0.14 ( 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 95 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 3 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7128 (mtpp) REVERT: l 3 LYS cc_start: 0.7227 (tmtt) cc_final: 0.6784 (tmtt) REVERT: m 7 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7668 (mptt) REVERT: T 3 LYS cc_start: 0.8468 (mtmm) cc_final: 0.7869 (mtpm) REVERT: t 3 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7043 (ttpp) REVERT: v 3 LYS cc_start: 0.8372 (mptt) cc_final: 0.7601 (mtpm) REVERT: 3 9 GLU cc_start: 0.8227 (mp0) cc_final: 0.7609 (mp0) REVERT: 8 9 GLU cc_start: 0.9166 (tt0) cc_final: 0.8816 (tt0) REVERT: AI 9 GLU cc_start: 0.8268 (mp0) cc_final: 0.8008 (mp0) REVERT: AV 2 PHE cc_start: 0.7672 (m-10) cc_final: 0.7408 (m-10) REVERT: AV 7 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8289 (mttm) REVERT: AX 7 LYS cc_start: 0.8847 (mtpm) cc_final: 0.8118 (mptp) REVERT: AY 9 GLU cc_start: 0.8352 (mp0) cc_final: 0.8033 (mp0) REVERT: AS 9 GLU cc_start: 0.9195 (tt0) cc_final: 0.8808 (tt0) REVERT: AU 7 LYS cc_start: 0.6239 (OUTLIER) cc_final: 0.4217 (tttm) REVERT: Ad 7 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7052 (tppt) outliers start: 27 outliers final: 15 residues processed: 79 average time/residue: 0.9314 time to fit residues: 75.6558 Evaluate side-chains 88 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 9 GLU Chi-restraints excluded: chain d residue 9 GLU Chi-restraints excluded: chain f residue 9 GLU Chi-restraints excluded: chain R residue 3 LYS Chi-restraints excluded: chain m residue 7 LYS Chi-restraints excluded: chain j residue 9 GLU 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 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 7 LYS Chi-restraints excluded: chain AK 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 7 LYS Chi-restraints excluded: chain AU 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: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.122859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100762 restraints weight = 8834.680| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.72 r_work: 0.3223 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.7702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6150 Z= 0.121 Angle : 0.697 8.683 7800 Z= 0.337 Chirality : 0.026 0.064 525 Planarity : 0.002 0.015 975 Dihedral : 53.604 179.968 675 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.29 % Allowed : 36.00 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHEAH 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 6075) covalent geometry : angle 0.69651 / 0.34 ( 7800) hydrogen bonds : bond 0.02996 / 1.65 ( 158) hydrogen bonds : angle 3.83831 / 2.48 ( 474) Misc. bond : bond 0.00029 / 0.02 ( 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 88 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.260 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: g 9 GLU cc_start: 0.8280 (mt-10) cc_final: 0.6546 (mp0) REVERT: m 7 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7465 (mptt) REVERT: T 3 LYS cc_start: 0.8405 (mtmm) cc_final: 0.7814 (mtpm) REVERT: u 9 GLU cc_start: 0.7785 (pm20) cc_final: 0.7551 (mp0) REVERT: v 3 LYS cc_start: 0.8170 (mptt) cc_final: 0.7395 (mtpm) REVERT: 3 9 GLU cc_start: 0.8095 (mp0) cc_final: 0.7584 (mp0) REVERT: 8 9 GLU cc_start: 0.8895 (tt0) cc_final: 0.8525 (tt0) REVERT: AA 3 LYS cc_start: 0.7777 (mtpm) cc_final: 0.7001 (tmtt) REVERT: AA 7 LYS cc_start: 0.7976 (mtpm) cc_final: 0.7151 (mmtt) REVERT: AB 3 LYS cc_start: 0.8260 (mptt) cc_final: 0.7887 (mppt) REVERT: AI 9 GLU cc_start: 0.8048 (mp0) cc_final: 0.7741 (mp0) REVERT: AD 9 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8364 (tt0) REVERT: AN 9 GLU cc_start: 0.8785 (tt0) cc_final: 0.8305 (tt0) REVERT: AL 3 LYS cc_start: 0.8757 (tttt) cc_final: 0.8549 (tttp) REVERT: AP 7 LYS cc_start: 0.7629 (mttp) cc_final: 0.7274 (mptp) REVERT: AY 9 GLU cc_start: 0.7953 (mp0) cc_final: 0.7572 (mp0) REVERT: AU 3 LYS cc_start: 0.8342 (ptmt) cc_final: 0.6080 (tptt) REVERT: Ad 7 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.6836 (tppt) REVERT: Ad 9 GLU cc_start: 0.8830 (tt0) cc_final: 0.8550 (tt0) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 1.0016 time to fit residues: 81.2279 Evaluate side-chains 83 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 9 GLU Chi-restraints excluded: chain R residue 3 LYS Chi-restraints excluded: chain m 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 4 residue 9 GLU Chi-restraints excluded: chain 9 residue 7 LYS Chi-restraints excluded: chain AO residue 7 LYS 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: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3574 r_free = 0.3574 target = 0.114302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.092354 restraints weight = 9366.053| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.67 r_work: 0.3040 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.7929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.053 6150 Z= 0.577 Angle : 0.970 8.663 7800 Z= 0.470 Chirality : 0.038 0.142 525 Planarity : 0.004 0.020 975 Dihedral : 53.359 179.978 675 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 4.38 % Allowed : 34.10 % Favored : 61.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.22), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE k 2 Details of bonding type rmsd/Z covalent geometry : bond 0.01457 / 0.58 ( 6075) covalent geometry : angle 0.97039 / 0.47 ( 7800) hydrogen bonds : bond 0.03850 / 2.23 ( 158) hydrogen bonds : angle 3.77041 / 2.37 ( 474) Misc. bond : bond 0.00231 / 0.14 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1859.30 seconds wall clock time: 32 minutes 30.43 seconds (1950.43 seconds total)